MolNFT v1 · #36883 · protein

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

2FJG · Vascular endothelial growth factor a: “Structure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.60). MolNFT v1 #36883 on GenesisL1: 3D…

PDB: 2FJG
Type: protein
Length: 1,047 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor a; Fab light chain; Fab heavy chain
UniProt: Q96NW5
Ligands: SO4
Pockets: 14 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V	Vascular endothelial growth factor a	protein	95	13% helix, 63% strand	Q96NW5
W	Vascular endothelial growth factor a	protein	94	13% helix, 64% strand	Q96NW5
L, A	Fab light chain	protein	211	7% helix, 51% strand	—
H, B	Fab heavy chain	protein	218	7% helix, 53% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B, H, L, W, V

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.60	0.74	59	empty
2	460	0.59	0.74	52	empty
3	123	0.52	0.81	24	empty
4	134	0.48	0.78	21	empty
5	101	0.42	0.77	25	empty

Interfaces

11 interfaces between chains.

A–B · 1927 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 1913 Å² buried · 12 hydrogen bonds · protein-protein
V–W · 1371 Å² buried · 14 hydrogen bonds · protein-protein
V–H · 403 Å² buried · 6 hydrogen bonds · protein-protein
W–B · 392 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

2FJG · Structure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF · the same entry in another collection · chain V against V, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q96NW5
Elsewhere: RCSB PDB 2FJG · PDBe 2FJG · UniProt Q96NW5

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