SMTL ID : 4kzn.1

crystal structure of human VEGF-A receptor binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 6 residues within 4Å: Chain A: Y.34, E.68, S.69, N.70, M.89, S.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.90, A:S.90, A:S.90 NAG-NAG-BMA-MAN-MAN-FUC.4: 6 residues within 4Å: Chain B: Y.34, E.68, S.69, N.70, M.89, S.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.34, B:S.90, B:S.90, B:S.90

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: I.78, K.79, P.80, H.81, Q.82, G.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.81 PGE.5: 6 residues within 4Å: Chain B: I.78, K.79, P.80, H.81, Q.82, G.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.81

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: C.55, C.56, N.57, D.58, L.61 Chain B: S.45 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.45, B:S.45, A:C.56, A:N.57, A:D.58, A:D.58 Water bridges: B:D.29 SO4.6: 6 residues within 4Å: Chain A: S.45 Chain B: C.55, C.56, N.57, D.58, L.61 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.56, B:N.57, B:D.58, B:D.58, A:S.45, A:S.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, S.T. et al., Structural Basis for the Bivalent Glycosylated Human VEGF-A121 and VEGF-A165 in recruiment of Receptor and Co-receptor. to be published

Release Date

2014-06-04

Peptides

Vascular endothelial growth factor A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Vascular endothelial growth factor A