MolNFT v1 · #19765 · protein

Vascular endothelial growth factor in complex with domain 2 of the flt-1 receptor

1QTY: “Vascular endothelial growth factor in complex with domain 2 of the flt-1 receptor”. X-ray diffraction, 8 pockets (best druggability 0.62). MolNFT v1 #19765 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QTY
Type: protein
Length: 757 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor; Fms-like tyrosine kinase 1
UniProt: P15692, P17948
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V, W, R	Vascular endothelial growth factor	protein	95	13% helix, 62% strand	P15692
S	Vascular endothelial growth factor	protein	96	13% helix, 64% strand	P15692
X, Y, T, U	Fms-like tyrosine kinase 1	protein	94	3% helix, 45% strand	P17948

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	458	0.62	0.76	45	empty
2	329	0.57	0.76	60	empty
3	145	0.50	0.79	29	empty
4	207	0.49	0.76	39	empty
5	105	0.49	0.81	20	empty

Interfaces

12 interfaces between chains.

V–W · 1379 Å² buried · 13 hydrogen bonds · protein-protein
R–S · 1365 Å² buried · 14 hydrogen bonds · protein-protein
R–U · 633 Å² buried · 3 hydrogen bonds · protein-protein
S–T · 615 Å² buried · 2 hydrogen bonds · protein-protein
W–X · 605 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

1QTY · Vascular endothelial growth factor in complex with domain 2 of the flt-1 receptor · the same entry in another collection · chain U against U, 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 V against A, TM-score 0.98
P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain X 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
Every structure of UniProt P17948
Elsewhere: RCSB PDB 1QTY · PDBe 1QTY · UniProt P15692 · UniProt P17948

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