Research workbench
VEGF-a 13:107 crystallized with 2C bicyclic peptide
Analyse VEGF-a 13:107 crystallized with 2C bicyclic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z3F
- Type
- protein
- Length
- 204 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: P; Vascular endothelial growth factor a
- UniProt
- P15692
- Ligands
- NH2
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Chains: P | protein | 14 | 29% helix, 0% strand | — |
| V, W | Vascular endothelial growth factor a | protein | 95 | 16% helix, 60% strand | P15692 |
Ligands and binding sites
- NH2 · Amino group · ion · chains P
- ACY · Acetic acid · additive · 5 copies · chains V, W
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains P, V
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.43 | 0.76 | 38 | empty |
| 2 | 74 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- V–W · 1393 Ų buried · 13 hydrogen bonds · protein-protein
- P–W · 412 Ų buried · 5 hydrogen bonds · protein-protein
- P–V · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 isopeptide, 1 modified (disulfide, isopeptide, nonstandard).
Compared structures
- 6Z3F · VEGF-A 13:107 crystallized with 2C bicyclic peptide · the same entry in another collection · chain P against P, TM-score 1.00
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 6Z3F · PDBe 6Z3F · UniProt P15692
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