SMTL ID : 5t89.1

Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain C: E.44, Q.72, N.74, H.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain D: R.157, N.170 No protein-ligand interaction detected (PLIP)

19 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.3: 5 residues within 4Å: Chain A: Y.49, N.85, S.105, F.106, L.107 Ligand excluded by PLIP NAG.4: 6 residues within 4Å: Chain B: E.48, Y.49, N.85, S.105, F.106, L.107 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain C: R.157, N.170, T.172 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain C: N.225 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain C: L.282, N.297 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain C: D.346, G.347, L.348, N.376 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain C: F.389, N.391 Ligands: NAG.12 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain C: N.521 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain C: G.544, D.546, M.598, N.599 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Ligands: NAG.9 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain D: Q.72, N.74 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain D: N.138 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: S.209, N.225, Y.267 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: L.282, N.297 Ligands: NAG.21 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain D: Q.316, N.376, T.395 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain D: N.391 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain D: N.521 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: G.544, D.546, M.598, N.599 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Ligands: NAG.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Markovic-Mueller, S. et al., Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A. Structure (2017)

Release Date

2017-02-01

Peptides

Vascular endothelial growth factor A: AB
Vascular endothelial growth factor receptor 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
W

C
X

D
Y

Vascular endothelial growth factor A

Vascular endothelial growth factor receptor 1