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VEGF-A 13:107 crystallized with 1C bicyclic peptide

Analyse VEGF-A 13:107 crystallized with 1C bicyclic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZCD
Type: protein
Length: 204 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Derived from V114 peptide; Vascular endothelial growth factor A
UniProt: P15692
Ligands: PO4
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · resolution 1.8 · 2 distinct chains · 17% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Derived from V114 peptide	protein	14	29% helix, 0% strand	—
V, W	Vascular endothelial growth factor A	protein	95	16% helix, 60% strand	P15692

Ligands and binding sites

PO4 · Phosphate ion · ion · chains W
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains P, V, W

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.40	0.77	26	empty
2	94	0.39	0.76	26	empty

Interfaces

3 interfaces between chains.

V–W · 1384 Å² buried · 12 hydrogen bonds · protein-protein
P–W · 419 Å² buried · 5 hydrogen bonds · protein-protein
P–V · 96 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 1 isopeptide, 1 modified (disulfide, isopeptide, nonstandard).

Compared structures

6ZCD · VEGF-a 13:107 crystallized with 1C bicyclic peptide · the same entry in another collection · chain P against P, 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 0.96

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 6ZCD · PDBe 6ZCD · UniProt P15692

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