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BMRB: 18755

2LZG

NMR Structure of Mdm2 (6-125) with Pip-1

Authors

Michelsen, K.B., Jordan, J.B., Lewis, J., Long, A.M., Yang, E., Rew, Y., Zhou, J., Yakowec, P., Schnier, P.D., Huang, X., Poppe, L.

Assembly

Mdm2 (6-125) with Pip-1

Entity

1. Mdm2 (6-125) with Pip-1, entity 1 (polymer, Thiol state: all free), 124 monomers, 14006.91 Da Detail

MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQIVYCSNDL LGDLFGVPSF SVKEHRKIYT MIYRNLVVVN QQESSDSGTS VSEN

2. {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid (non-polymer), 478.408 × 2 Da

Total weight

14963.727 Da

Max. entity weight

14006.91 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics, DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.2 %, Completeness: 73.7 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.7 % (1077 of 1462)	70.0 % (532 of 760)	75.2 % (428 of 569)	88.0 % (117 of 133)
Backbone	91.7 % (673 of 734)	91.6 % (228 of 249)	90.4 % (331 of 366)	95.8 % (114 of 119)
Sidechain	60.5 % (512 of 846)	59.5 % (304 of 511)	63.9 % (205 of 321)	21.4 % (3 of 14)
Aromatic	20.0 % (18 of 90)	26.7 % (12 of 45)	13.3 % (6 of 45)
Methyl	84.2 % (123 of 146)	86.3 % (63 of 73)	82.2 % (60 of 73)

1. entity 1

MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQIVYCSNDL LGDLFGVPSF SVKEHRKIYT MIYRNLVVVN QQESSDSGTS VSEN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.36 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.36 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: 0.51 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 5 models in PDB: 2LZG, Strand ID: A Detail

Release date

2012-11-01

Citation

Ordering of the N-terminus of human MDM2 by small molecule inhibitors
Michelsen, K., Jordan, J.B., Lewis, J., Long, A.M., Yang, E., Rew, Y., Zhou, J., Yakowec, P., Schnier, P.D., Huang, X., Poppe, L.
J. Am. Chem. Soc. (2012), 134, 17059-17067, PubMed 22991965 , DOI 10.1021/ja305839b , Abstract

Related entities 1. Mdm2 (6-125) with Pip-1, entity 1, : 1 : 56 entities Detail

Interaction partners 1. Mdm2 (6-125) with Pip-1, entity 1, : 170 interactors Detail

More details for 170 interactors identified by 57 citations

Experiments performed 8 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288.15 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		500 uM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	DTT	[U-100% 2H]		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18755_2lzg.nef
Input source #2: Coordindates	2lzg.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	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	13Q	[(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-(cyclopropylmethyl)-2-oxopiperidin-3-yl]acetic acid	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIY

-------110-------120-----
TMIYRNLVVVNQQESSDSGTSVSEN
|||||||||||||||||||||||||
TMIYRNLVVVNQQESSDSGTSVSEN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_18755_2lzg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1007		93.6 (chain: A, length: 125)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3761 (1)	noe	89.6 (chain: A, length: 125)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	62 (1)	hbond	37.6 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 93.6%
- Total number of assignments
  - ¹H chemical shifts: 489
  - ¹⁵N chemical shifts: 113
  - ¹³C chemical shifts: 405
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 89.6%
- Total number of restraints: 3758
- Weight of restraints: 1.0 (3758)
- Potential type of restraints: upper-bound-parabolic (3758)
- Range of distance target values: 2.24, 6.17 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 37.6%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: upper-bound-parabolic (62)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Keywords Mdm2