MolNFT v1 · #171325 · protein
VEGF-a 13:107 crystallized with 3C bicyclic peptide
6Z13 · Bicyclic peptide 3C: “VEGF-a 13:107 crystallized with 3C bicyclic peptide”. X-ray diffraction, 1 ligand (NH2), 2 pockets (best druggability 0.34). MolNFT v1 #171325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z13
- Type
- protein
- Length
- 205 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bicyclic peptide 3C; Vascular endothelial growth factor a
- UniProt
- P15692
- Ligands
- NH2
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Bicyclic peptide 3C | protein | 15 | 20% 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, V
- ACY · Acetic acid · additive · 5 copies · chains V, W, P
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains 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 | 97 | 0.34 | 0.74 | 28 | empty |
| 2 | 69 | 0.34 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- V–W · 1401 Ų buried · 16 hydrogen bonds · protein-protein
- P–W · 406 Ų buried · 6 hydrogen bonds · protein-protein
- P–V · 172 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 isopeptide, 1 modified (disulfide, isopeptide, nonstandard).
Compared structures
- 6Z13 · VEGF-A 13:107 crystallized with 3C 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 6Z13 · PDBe 6Z13 · UniProt P15692
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