Research workbench

Vascular endothelial growth factor refined to 1.93 ångströms resolution

Analyse Vascular endothelial growth factor refined to 1.93 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VPF
Type: protein
Length: 762 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor
UniProt: P15692
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vascular endothelial growth factor	protein	97	12% helix, 60% strand	P15692
B, E, F	Vascular endothelial growth factor	protein	96	13% helix, 60% strand	P15692
C	Vascular endothelial growth factor	protein	93	12% helix, 62% strand	P15692
D, G	Vascular endothelial growth factor	protein	95	12% helix, 61% strand	P15692
H	Vascular endothelial growth factor	protein	94	13% helix, 62% strand	P15692

Pockets

8 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	488	0.68	0.79	75	empty
2	113	0.58	0.85	22	empty
3	278	0.52	0.75	61	empty
4	266	0.52	0.75	35	empty
5	94	0.40	0.77	16	empty

Interfaces

12 interfaces between chains.

G–H · 1414 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1412 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1380 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1351 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 435 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 31 disulfide (disulfide).

Compared structures

2VPF · Vascular endothelial growth factor refined to 1.93 ångströms resolution · the same entry in another collection · chain H against H, TM-score 1.00
P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P15692
Elsewhere: RCSB PDB 2VPF · PDBe 2VPF · UniProt P15692

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.