SMTL ID : 4ckv.1

Crystal structure of VEGFR-1 domain 2 in presence of Zn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.16, H.92 Chain B: H.16, H.92 Ligands: ZN.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.16, A:H.92, B:H.16, B:H.92 ZN.6: 5 residues within 4Å: Chain A: H.16, H.92 Chain B: H.16, H.92 Ligands: ZN.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.16, A:H.92, B:H.16, B:H.92

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: T.79, V.80, N.81, G.82 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.82 EDO.3: 4 residues within 4Å: Chain A: T.35, A.78, T.79 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.35, A:T.79 Water bridges: A:T.37 EDO.4: 2 residues within 4Å: Chain A: R.21, E.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.22 EDO.5: 7 residues within 4Å: Chain A: N.33, I.34, T.35, T.79, V.80 Ligands: EDO.2, EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.35, A:T.35 EDO.7: 5 residues within 4Å: Chain B: T.79, V.80, N.81, G.82 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.82 EDO.8: 4 residues within 4Å: Chain B: T.35, A.78, T.79 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.35, B:T.79, B:T.79 EDO.9: 2 residues within 4Å: Chain B: R.21, E.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.22 EDO.10: 7 residues within 4Å: Chain B: N.33, I.34, T.35, T.79, V.80 Ligands: EDO.7, EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.35, B:T.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaucher, J.-F. et al., Biophysical Studies of the Induced Dimerization of Human Vegf R Receptor 1 Binding Domain by Divalent Metals Competing with Vegf-A. Plos One (2016)

Release Date

2015-01-28

Peptides

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1

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