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BMRB: 25288

2MVW

Solution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)

Authors

Huang, S., Naik, M.T., Fan, P., Wang, Y., Chang, C., Huang, T.

Assembly

TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)

Entity

1. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity 1 (polymer, Thiol state: all other bound), 51 monomers, 5933.728 × 2 Da Detail

GSRQIVDAQA VCTRCKESAD FWCFECEQLL CAKCFEAHQW FLKHEARPLA E

2. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity ZN (non-polymer), 65.409 × 4 Da

Total weight

12129.092 Da

Max. entity weight

5933.728 Da

Entity Connection

metal coordination 16 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS12:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS15:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS31:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS34:SG	2:ZN1:ZN
5	metal coordination	sing	1:CYS23:SG	2:ZN1:ZN
6	metal coordination	sing	1:CYS26:SG	2:ZN1:ZN
7	metal coordination	sing	1:HIS38:NE2	2:ZN1:ZN
8	metal coordination	sing	1:HIS44:NE2	2:ZN1:ZN
9	metal coordination	sing	1:CYS12:SG	2:ZN1:ZN
10	metal coordination	sing	1:CYS15:SG	2:ZN1:ZN
11	metal coordination	sing	1:CYS31:SG	2:ZN1:ZN
12	metal coordination	sing	1:CYS34:SG	2:ZN1:ZN
13	metal coordination	sing	1:CYS23:SG	2:ZN1:ZN
14	metal coordination	sing	1:CYS26:SG	2:ZN1:ZN
15	metal coordination	sing	1:HIS38:NE2	2:ZN1:ZN
16	metal coordination	sing	1:HIS44:NE2	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.9 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.9 % (535 of 602)	94.9 % (297 of 313)	79.0 % (184 of 233)	96.4 % (54 of 56)
Backbone	81.6 % (248 of 304)	94.1 % (96 of 102)	68.4 % (104 of 152)	96.0 % (48 of 50)
Sidechain	96.8 % (337 of 348)	95.3 % (201 of 211)	99.2 % (130 of 131)	100.0 % (6 of 6)
Aromatic	90.3 % (65 of 72)	83.3 % (30 of 36)	97.1 % (33 of 34)	100.0 % (2 of 2)
Methyl	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)

1. entity 1

GSRQIVDAQA VCTRCKESAD FWCFECEQLL CAKCFEAHQW FLKHEARPLA E

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
7	TRIS	[U-98% 2H]	25 mM
8	sodium chloride	natural abundance	100 mM
9	TCEP	natural abundance	0.2 mM
10	zinc chloride	natural abundance	1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	PML B1 box	[U-99% 13C; U-99% 15N]	0.5 mM
12	PML B1 box	natural abundance	0.5 mM
13	TRIS	[U-98% 2H]	25 mM
14	sodium chloride	natural abundance	100 mM
15	TCEP	natural abundance	0.2 mM
16	zinc chloride	natural abundance	1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MVW, Strand ID: A, B Detail

Release date

2015-08-24

Citation

The B-box 1 dimer of human promyelocytic leukemia protein
Huang, S., Naik, M.T., Wang, Y., Chang, C., Fan, P., Shih, H., Huang, T.
J. Biomol. NMR (2014), 60, 275-281, PubMed 25355412 , DOI 10.1007/s10858-014-9869-4 , Abstract

Related entities 1. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity 1, : 1 : 1 : 2 : 25 entities Detail

Interaction partners 1. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity 1, : 79 interactors Detail

More details for 79 interactors identified by 50 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

2 2D 1H-13C HSQC

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

3 3D CBCA(CO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

4 3D HNCO

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

5 3D HNCA

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

6 3D H(CCO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

7 3D C(CO)NH

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

8 3D 1H-15N TOCSY

Instrument

Bruker Uniform NMR System - 600 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

9 3D 1H-15N NOESY

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

10 2D 1H-1H COSY

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

11 2D 1H-1H NOESY

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
2	TRIS	[U-98% 2H]	25 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	0.2 mM
5	zinc chloride	natural abundance	1 mM

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker Uniform NMR System - 800 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	PML B1 box	[U-99% 13C; U-99% 15N]	1 mM
7	TRIS	[U-98% 2H]	25 mM
8	sodium chloride	natural abundance	100 mM
9	TCEP	natural abundance	0.2 mM
10	zinc chloride	natural abundance	1 mM

14 13C-edited/12C-filtered 3D NOESY-HSQC

Instrument

Bruker Uniform NMR System - 850 MHz equipped with a cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	PML B1 box	[U-99% 13C; U-99% 15N]	0.5 mM
12	PML B1 box	natural abundance	0.5 mM
13	TRIS	[U-98% 2H]	25 mM
14	sodium chloride	natural abundance	100 mM
15	TCEP	natural abundance	0.2 mM
16	zinc chloride	natural abundance	1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25288_2mvw.nef
Input source #2: Coordindates	2mvw.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:44:HIS:NE2	3:4:ZN:ZN	unknown	unknown	n/a
2:38:HIS:NE2	3:4:ZN:ZN	unknown	unknown	n/a
1:44:HIS:ND1	3:2:ZN:ZN	unknown	unknown	n/a
1:44:HIS:NE2	3:2:ZN:ZN	unknown	unknown	n/a
1:38:HIS:NE2	3:2:ZN:ZN	unknown	unknown	n/a
2:23:CYS:SG	3:4:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:34:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:31:CYS:SG	3:3:ZN:ZN	unknown	unknown	n/a
1:15:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:26:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:31:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:12:CYS:SG	3:3:ZN:ZN	unknown	unknown	n/a
2:26:CYS:SG	3:4:ZN:ZN	unknown	unknown	n/a
2:15:CYS:SG	3:3:ZN:ZN	unknown	unknown	n/a
2:34:CYS:SG	3:3:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	Distance restraints
C	2	ZN	ZINC ION	None
C	3	ZN	ZINC ION	None
C	4	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--120-----130-------140-------150-------160--------
GSRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAE
|||||||||||||||||||||||||||||||||||||||||||||||||||
GSRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAE
--------10--------20--------30--------40--------50-

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--120-----130-------140-------150-------160--------
GSRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAE
|||||||||||||||||||||||||||||||||||||||||||||||||||
GSRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAE
--------10--------20--------30--------40--------50-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	51	0	0	100.0
B	B	51	0	0	100.0

Content subtype: combined_25288_2mvw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	17		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	540		100.0 (chain: A, length: 51)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1929 (1)	noe	96.1 (chain: A, length: 51), 96.1 (chain: B, length: 51)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Error	16 (1)	undefined	15.7 (chain: A, length: 51), 15.7 (chain: B, length: 51), 25.0 (chain: C, length: 4)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	27 (1)	hbond	23.5 (chain: A, length: 51), 23.5 (chain: B, length: 51)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	84 (84)	.	70.6 (chain: A, length: 51), 66.7 (chain: B, length: 51)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 305
  - ¹³C chemical shifts: 181
  - ¹⁵N chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	313	305	97.4
¹³C chemical shifts	233	181	77.7
¹⁵N chemical shifts	59	54	91.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	97	95.1
¹³C chemical shifts	102	51	50.0
¹⁵N chemical shifts	50	47	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	208	98.6
¹³C chemical shifts	131	130	99.2
¹⁵N chemical shifts	9	7	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0
¹³C chemical shifts	22	22	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	35	97.2
¹³C chemical shifts	34	33	97.1
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 96.1%
  - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 96.1%
- Total number of restraints: 1922
- Weight of restraints: 1.0 (1922)
- Potential type of restraints: square-well-parabolic (1922)
- Range of distance target values: 1.34, 3.1 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 15.7%
    - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 15.7%
    - Entity_assembly_ID: C, Chain length: 4, Sequence coverage: 25.0%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: square-well-parabolic (16)
  - Range of distance target values: 2.4, 2.6 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 23.5%
      - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 23.5%
    - Total number of restraints: 27
    - Weight of restraints: 1.0 (27)
    - Potential type of restraints: square-well-parabolic (27)
    - Range of distance target values: 2.12, 3.13 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 70.6%
  - Entity_assembly_ID: B, Chain length: 51, Sequence coverage: 66.7%
- Total number of restraints: 84
- Total number of restraints per polymer type: 84
- Weight of restraints: 1.0 (84)
- Potential type of restraints: square-well-parabolic (84)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords B box, E3 ligase, METAL BINDING PROTEIN, PML, TRIM19

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Found 1 Document (1.542 seconds)

BMRB: 25288

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity 1, : 1 : 1 : 2 : 25 entities Detail

Interaction partners 1. TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML), entity 1, : 79 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 6 contents Detail