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Structure of bevacizumab Fab mutant in complex with VEGF

Analyse Structure of bevacizumab Fab mutant in complex with VEGF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BFT
Type: protein
Length: 1,057 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avastin light chain Fab fragment mutant; Avastin heavy chain Fab fragment mutant…
UniProt: Q8TCD0, P0DOX5, P15692
Ligands: SO4
Pockets: 12 · best druggability 0.57

Structure

x-ray diffraction · 6 distinct chains · 9% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Avastin light chain Fab fragment mutant	protein	214	7% helix, 51% strand	Q8TCD0
A	Avastin heavy chain Fab fragment mutant	protein	224	9% helix, 50% strand	P0DOX5
L	Avastin light chain Fab fragment mutant	protein	213	6% helix, 52% strand	Q8TCD0
H	Avastin heavy chain Fab fragment mutant	protein	217	10% helix, 51% strand	P0DOX5
G	Vascular endothelial growth factor a	protein	95	13% helix, 64% strand	P15692
C	Vascular endothelial growth factor a	protein	94	13% helix, 64% strand	P15692

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, L
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains H, G

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	405	0.57	0.74	48	empty
2	379	0.56	0.74	51	empty
3	197	0.54	0.78	35	empty
4	68	0.52	0.86	23	empty
5	119	0.39	0.74	22	empty

Interfaces

9 interfaces between chains.

B–A · 1981 Å² buried · 20 hydrogen bonds · protein-protein
L–H · 1696 Å² buried · 17 hydrogen bonds · protein-protein
G–C · 1338 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 808 Å² buried · 18 hydrogen bonds · protein-protein
H–C · 803 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 2 modified (disulfide, oxidation).

Compared structures

6BFT · Structure of Bevacizumab Fab mutant in complex with VEGF · the same entry in another collection · chain B against B, 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 Q8TCD0
Every structure of UniProt P0DOX5
Every structure of UniProt P15692
Elsewhere: RCSB PDB 6BFT · PDBe 6BFT · UniProt Q8TCD0 · UniProt P0DOX5 · UniProt P15692

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