SMTL ID : 2xv7.1

Crystal structure of vascular endothelial growth factor D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA.1: 10 residues within 4Å: Chain A: R.52, N.66, T.67, S.68, T.69, Y.71, A.95, H.97 Ligands: MAN.3, MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.71 NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: P.24, F.51, S.70, I.72, N.96, H.97, T.98 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.51 NAG-NAG-BMA.5: 10 residues within 4Å: Chain B: R.52, N.66, T.67, S.68, T.69, Y.71, A.95, H.97 Ligands: MAN.7, MAN.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.71 NAG-NAG-BMA.6: 7 residues within 4Å: Chain B: P.24, F.51, S.70, I.72, N.96, H.97, T.98 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.51

4 x MAN: alpha-D-mannopyranose(Non-functional Binders)(Non-covalent)

MAN.3: 1 residues within 4Å: Ligands: NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) MAN.4: 3 residues within 4Å: Chain A: L.35, G.36 Ligands: NAG-NAG-BMA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.36 MAN.7: 1 residues within 4Å: Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) MAN.8: 3 residues within 4Å: Chain B: L.35, G.36 Ligands: NAG-NAG-BMA.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leppanen, V.M. et al., Structural Determinants of Vascular Endothelial Growth Factor-D - Receptor Binding and Specificity. Blood (2011)

Release Date

2011-01-12

Peptides

VASCULAR ENDOTHELIAL GROWTH FACTOR D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

VASCULAR ENDOTHELIAL GROWTH FACTOR D