MolNFT v1 · #134574 · protein

Crystal structure of VEGF-a in complex with vegfr-1 domains D1-6

5T89 · Vascular endothelial growth factor a: “Crystal structure of VEGF-a in complex with vegfr-1 domains D1-6”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.74). MolNFT v1 #134574 on GenesisL1: 3D structure, binding…

PDB: 5T89
Type: protein
Length: 1,385 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor a; Vascular endothelial growth factor receptor 1
EC: 2.7.10.1
UniProt: P15692, P17948
Ligands: NAG
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V, W	Vascular endothelial growth factor a	protein	96	13% helix, 60% strand	P15692
X	Vascular endothelial growth factor receptor 1 (EC 2.7.10.1)	protein	596	3% helix, 46% strand	P17948
Y	Vascular endothelial growth factor receptor 1 (EC 2.7.10.1)	protein	597	2% helix, 47% strand	P17948

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains X, Y, V, W

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	817	0.74	0.78	58	empty
2	159	0.63	0.85	29	empty
3	91	0.53	0.84	16	empty
4	150	0.52	0.79	28	empty
5	212	0.52	0.77	29	empty

Interfaces

6 interfaces between chains.

V–W · 1419 Å² buried · 14 hydrogen bonds · protein-protein
X–Y · 1148 Å² buried · 14 hydrogen bonds · protein-protein
V–X · 887 Å² buried · 2 hydrogen bonds · protein-protein
W–Y · 840 Å² buried · 3 hydrogen bonds · protein-protein
W–X · 802 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 glycan, 18 disulfide (N-glycosylation, disulfide, glycosylation).

Compared structures

P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain Y against A, TM-score 0.81

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
Every structure of UniProt P17948
Elsewhere: RCSB PDB 5T89 · PDBe 5T89 · UniProt P15692 · UniProt P17948

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