BMRBj - BMREntryMaster

Found 1 Document (4.224 seconds)

BMRB: 7131

2CNJ

Solution structure of IGF2R domain 11

Authors

Williams, C., Crump, M.P.

Assembly

IGF2R domain 11

Entity

1. IGF2R domain 11 (polymer, Thiol state: all disulfide bound), 151 monomers, 16627.64 Da Detail

MKSNEHDDCQ VTNPSTGHLF DLSSLSGRAG FTAAYSEKGL VYMSICGENE NCPPGVGACF GQTRISVGKA NKRLRYVDQV LQLVYKDGSP CPSKSGLSYK SVISFVCRPE AGPTNRPMLI SLDKQTCTLF FSWHTPLACE QATEKHHHHH H

Formula weight

16627.64 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS9:SG	1:CYS46:SG
2	disulfide	sing	1:CYS107:SG	1:CYS139:SG
3	disulfide	sing	1:CYS91:SG	1:CYS127:SG
4	disulfide	sing	1:CYS59:SG	1:CYS52:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

WATER REFINED IN CNS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 88.8 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.8 % (1514 of 1705)	88.4 % (782 of 885)	88.6 % (589 of 665)	92.3 % (143 of 155)
Backbone	95.7 % (850 of 888)	95.7 % (292 of 305)	95.5 % (421 of 441)	96.5 % (137 of 142)
Sidechain	83.4 % (797 of 956)	84.5 % (490 of 580)	82.9 % (301 of 363)	46.2 % (6 of 13)
Aromatic	43.2 % (64 of 148)	44.6 % (33 of 74)	41.1 % (30 of 73)	100.0 % (1 of 1)
Methyl	100.0 % (134 of 134)	100.0 % (67 of 67)	100.0 % (67 of 67)

1. domain 11

MKSNEHDDCQ VTNPSTGHLF DLSSLSGRAG FTAAYSEKGL VYMSICGENE NCPPGVGACF GQTRISVGKA NKRLRYVDQV LQLVYKDGSP CPSKSGLSYK SVISFVCRPE AGPTNRPMLI SLDKQTCTLF FSWHTPLACE QATEKHHHHH H

Show sample condition

Sample

Temperature 298 K, pH 5.5 (±0.1), Details 600ul

#	Name	Isotope labeling	Concentration
1	domain 11	[U-95% 13C; U-95% 15N]	1 (±0.1) mM
2	NaOAc		20 mM
3	EDTA		1 mM
4	benzamidine		1 mM
5	NaN3		100 uM
6	NaN3		5 %

LACS Plot; CA

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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.16 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2CNJ, Strand ID: D Detail

Release date

2008-08-12

Citation

Structural insights into the interaction of insulin-like growth factor 2 with IGF2R domain 11
Williams, C., Rezgui, D., Prince, S.N., Zaccheo, O.J., Foulstone, E.J., Forbes, B.E., Norton, R.S., Crosby, J., Hassan, A.BASSIM., Crump, M.P.
Structure (2007), 15, 1065-1078, PubMed 17850746 , DOI 10.1016/j.str.2007.07.007 , Abstract

Related entities 1. IGF2R domain 11, : 1 : 10 : 97 entities Detail

Interaction partners 1. IGF2R domain 11, : 39 interactors Detail

More details for 39 interactors identified by 15 citations

Experiments performed 14 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr7131_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:9:CYS:SG	1:46:CYS:SG	oxidized, CA 58.164, CB 41.332 ppm	oxidized, CA 56.249, CB 41.057 ppm	n/a
1:107:CYS:SG	1:139:CYS:SG	oxidized, CA 57.013, CB 38.566 ppm	oxidized, CA 54.223, CB 42.308 ppm	n/a
1:91:CYS:SG	1:127:CYS:SG	oxidized, CA 51.681, CB 42.348 ppm	oxidized, CA 58.84, CB 40.416 ppm	n/a
1:59:CYS:SG	1:52:CYS:SG	oxidized, CA 55.702, CB 42.95 ppm	oxidized, CA 50.545, CB 39.307 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr7131_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	1641		97.4 (chain: 1, length: 151)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 151, Sequence coverage: 97.4%
- Total number of assignments
  - ¹³C chemical shifts: 595
  - ¹H chemical shifts: 899
  - ¹⁵N chemical shifts: 147
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
28	ARG	CZ	160.51
38	LYS	HZ1	6.855
38	LYS	HZ2	6.855
38	LYS	HZ3	6.855
64	ARG	CZ	160.042
73	ARG	CZ	160.534
75	ARG	CZ	160.441
116	ARG	CZ	160.587

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	665	590	88.7
¹H chemical shifts	885	760	85.9
¹⁵N chemical shifts	161	147	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	302	289	95.7
¹H chemical shifts	305	293	96.1
¹⁵N chemical shifts	142	137	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	363	301	82.9
¹H chemical shifts	580	467	80.5
¹⁵N chemical shifts	19	10	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	70	68	97.1
¹H chemical shifts	70	68	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	73	31	42.5
¹H chemical shifts	74	36	48.6
¹⁵N chemical shifts	1	1	100.0

Keywords cancer, IGF2R, IGF-II, NMR structure

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Found 1 Document (4.224 seconds)

BMRB: 7131

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. IGF2R domain 11, : 1 : 10 : 97 entities Detail

Interaction partners 1. IGF2R domain 11, : 39 interactors Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Chemical shift validation 3 contents Detail