SMTL ID : 2fjg.2 (1 other biounit)

Structure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain D: F.27, T.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.28, D:T.28, D:T.28 SO4.2: 6 residues within 4Å: Chain C: Y.55 Chain D: V.2, R.98, F.102, D.108, Y.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.108 Salt bridges: D:R.98 SO4.3: 3 residues within 4Å: Chain B: Q.15 Chain D: Y.57, T.58 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.58 SO4.4: 5 residues within 4Å: Chain F: V.2, R.98, F.102, D.108, Y.109 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.109 Salt bridges: F:R.98 SO4.5: 2 residues within 4Å: Chain F: F.27, T.28 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.28, F:D.31 SO4.6: 3 residues within 4Å: Chain A: Q.15 Chain F: Y.57, T.58 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.58 SO4.7: 3 residues within 4Å: Chain F: T.123, K.124, G.125 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.125 Salt bridges: F:K.124 SO4.8: 2 residues within 4Å: Chain J: F.27, T.28 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.28, J:T.28 SO4.9: 6 residues within 4Å: Chain I: Y.55 Chain J: V.2, R.98, F.102, D.108, Y.109 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Y.109, I:Y.55 Salt bridges: J:R.98 SO4.10: 3 residues within 4Å: Chain H: Q.15 Chain J: Y.57, T.58 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.58, J:T.58 SO4.11: 5 residues within 4Å: Chain L: V.2, R.98, F.102, D.108, Y.109 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:Y.109, L:Y.109 Salt bridges: L:R.98 SO4.12: 2 residues within 4Å: Chain L: F.27, T.28 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:T.28, L:T.28 SO4.13: 3 residues within 4Å: Chain G: Q.15 Chain L: Y.57, T.58 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:T.58, L:T.58 SO4.14: 3 residues within 4Å: Chain L: T.123, K.124, G.125 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:G.125 Salt bridges: L:K.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuh, G. et al., Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin Fab. J.Biol.Chem. (2006)

Release Date

2006-02-07

Peptides

Vascular endothelial growth factor A: ABGH
Fab light chain: CEIK
Fab heavy chain: DFJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
W

G
V

H
W

C
L

E
A

I
L

K
A

D
H

F
B

J
H

L
B

Vascular endothelial growth factor A

Fab light chain

Fab heavy chain

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