SMTL ID : 3s35.1

Structural basis for the function of two anti-VEGF receptor antibodies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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: 5 residues within 4Å: Chain B: Y.32, G.33 Chain C: S.13, N.29, L.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.32, B:G.33 Water bridges: B:S.31

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.100, D.105 Chain C: K.55 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.105, H2O.5, H2O.13 CA.3: 1 residues within 4Å: Chain A: D.66 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, H2O.2 CA.4: 3 residues within 4Å: Chain B: D.1, E.27, E.97 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.27, B:E.97, H2O.10 CA.5: 2 residues within 4Å: Chain B: D.98 Chain C: G.23 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, H2O.7, H2O.7, H2O.8 CA.7: 2 residues within 4Å: Chain C: G.4, E.35 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.35, H2O.13, H2O.14, H2O.15 CA.8: 1 residues within 4Å: Chain C: E.19 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.19, C:E.19, H2O.13, H2O.15

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

NAG.6: 5 residues within 4Å: Chain C: D.9, V.10, V.11, K.101, N.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.10, C:N.102 Water bridges: C:L.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franklin, M.C. et al., The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies. Structure (2011)

Release Date

2011-08-24

Peptides

6.64 Fab heavy chain: A
6.64 Fab light chain: B
Vascular endothelial growth factor receptor 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
X

6.64 Fab heavy chain

6.64 Fab light chain

Vascular endothelial growth factor receptor 2

Related Entries With Identical Sequence