BMRB: 5185

1H, 13C, and 15N resonance assignment of the vascular endothelial growth factor receptor-binding domain in complex with a receptor-blocking peptide

Authors

Pan, B., Fairbrother, W.J.

Assembly

vascular endothelial growth factor receptor-binding domain dimer in complex with peptide v107

Entity

1. vascular endothelial growth factor (polymer, Thiol state: all disulfide bound), 99 monomers, 11633.26 × 2 Da Detail

HHEVVKFMDV YQRSYCHPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCGGC CNDEGLECVP TEESNITMQI MRIKPHQGQH IGEMSFLQHN KCECRPKKD

2. v107 peptide (polymer, Thiol state: all disulfide bound), 19 monomers, 2344.603 × 2 Da Detail

GGNECDIARM WEWECFERL

Total weight

27955.727 Da

Max. entity weight

11633.26 Da

Entity Connection

disulfide 10 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS16:SG	1:CYS58:SG
2	disulfide	sing	0:CYS47:SG	1:CYS92:SG
3	disulfide	sing	0:CYS51:SG	1:CYS94:SG
4	disulfide	sing	0:CYS41:SG	1:CYS50:SG
5	disulfide	sing	0:CYS16:SG	1:CYS58:SG
6	disulfide	sing	0:CYS47:SG	1:CYS92:SG
7	disulfide	sing	0:CYS51:SG	1:CYS94:SG
8	disulfide	sing	0:CYS41:SG	1:CYS50:SG
9	disulfide	sing	0:CYS5:SG	2:CYS15:SG
10	disulfide	sing	0:CYS5:SG	2:CYS15:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

Torsion angle dynamics simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.7 %, Completeness: 79.6 %, Completeness (bb): 80.7 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	79.6 % (1123 of 1411)	78.8 % (586 of 744)	80.9 % (440 of 544)	78.9 % (97 of 123)
Backbone	80.7 % (560 of 694)	78.4 % (185 of 236)	82.7 % (287 of 347)	79.3 % (88 of 111)
Sidechain	79.3 % (657 of 828)	79.1 % (402 of 508)	79.9 % (246 of 308)	75.0 % (9 of 12)
Aromatic	55.4 % (72 of 130)	55.4 % (36 of 65)	57.1 % (36 of 63)	0.0 % (0 of 2)
Methyl	88.6 % (78 of 88)	88.6 % (39 of 44)	88.6 % (39 of 44)

1. vascular endothelial growth factor

HHEVVKFMDV YQRSYCHPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCGGC CNDEGLECVP TEESNITMQI MRIKPHQGQH IGEMSFLQHN KCECRPKKD

2. v107 peptide

GGNECDIARM WEWECFERL

Show sample condition

Sample

Temperature 318 (±0.2) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	vascular endothelial growth factor	[U-98% 13C; U-98% 15N]		2.0 mM
2	v107 peptide			2.25 mM
3	H2O			90 %
4	D2O			10 %

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LACS Plot; CA

Referencing offset: -0.28 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495

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LACS Plot; CB

Referencing offset: -0.28 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495

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LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 6 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495

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LACS Plot; CO

Referencing offset: 0.54 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495

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Protein Blocks Logo

Calculated from 24 models in PDB: 1KAT, Strand ID: V, W, X, Y Detail

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Release date

2002-05-06

Citation

1H, 13C, and 15N resonance assignment of the vascular endothelial growth factor receptor-binding domain in complex with a receptor-blocking peptide
Pan, B., Fairbrother, W.J.
J. Biomol. NMR (2002), 22, 189-190, PubMed 11883783 , Abstract

Related entities 1. vascular endothelial growth factor, : 2 : 1 : 82 entities Detail

Related entities 2. v107 peptide, : 1 entities Detail

Interaction partners 1. vascular endothelial growth factor, : 19 interactors Detail