MolNFT v1 · #171659 · protein
VEGF-a 13:107 crystallized with 1C bicyclic peptide
6ZCD · Derived from V114 peptide: “VEGF-a 13:107 crystallized with 1C bicyclic peptide”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.40). MolNFT v1 #171659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZCD
- Type
- protein
- Length
- 204 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Derived from V114 peptide; Vascular endothelial growth factor a
- UniProt
- P15692
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 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.
| Volume (ų) | 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 Ų buried · 12 hydrogen bonds · protein-protein
- P–W · 419 Ų buried · 5 hydrogen bonds · protein-protein
- P–V · 96 Ų 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
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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