MolNFT v1 · #87163 · protein

Crystal structure of VEGF-C in complex with vegfr-3 domains D1-2

4BSK · Vascular endothelial growth factor receptor 3: “Crystal structure of VEGF-C in complex with vegfr-3 domains D1-2”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.66). MolNFT v1 #87163 on GenesisL1: 3D structure…

PDB: 4BSK
Type: protein
Length: 270 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vascular endothelial growth factor receptor 3; Vascular endothelial growth factor C
EC: 2.7.10.1
UniProt: P35916, P49767
Ligands: NAG
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vascular endothelial growth factor receptor 3 (EC 2.7.10.1)	protein	172	4% helix, 34% strand	P35916
C	Vascular endothelial growth factor C	protein	98	19% helix, 51% strand	P49767

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, A

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

Pockets

5 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	251	0.66	0.83	34	empty
2	123	0.55	0.83	28	empty
3	78	0.44	0.80	16	empty
4	86	0.38	0.76	19	empty
5	116	0.37	0.74	17	empty

Interfaces

1 interface between chains.

A–C · 258 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

4BSK · Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2 · the same entry in another collection · chain A against A, TM-score 1.00
P49767 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor C (P49767) · a predicted model of the same protein · chain C against A, TM-score 0.94
P35916 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 3… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P35916
Every structure of UniProt P49767
Elsewhere: RCSB PDB 4BSK · PDBe 4BSK · UniProt P35916 · UniProt P49767

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