MolNFT v1 · #74887 · protein
Crystal structure of an engineered human autonomous vh domain in complex with VEGF
3P9W · Vascular endothelial growth factor a: “Crystal structure of an engineered human autonomous vh domain in complex with VEGF”. X-ray diffraction, 10 pockets (best druggability 0.66). MolNFT v1 #74887 on GenesisL1: 3D structure, binding…
- PDB
- 3P9W
- Type
- protein
- Length
- 875 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; Human VEGF
- UniProt
- P15692
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor a | protein | 96 | 13% helix, 60% strand | P15692 |
| B | Human VEGF | protein | 123 | 7% helix, 54% strand | — |
| C, E | Vascular endothelial growth factor a | protein | 97 | 15% helix, 63% strand | P15692 |
| D | Human VEGF | protein | 121 | 7% helix, 54% strand | — |
| F, H | Human VEGF | protein | 122 | 10% helix, 54% strand | — |
| G | Vascular endothelial growth factor a | protein | 97 | 12% helix, 61% strand | P15692 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.66 | 0.80 | 63 | empty |
| 2 | 165 | 0.44 | 0.74 | 25 | empty |
| 3 | 98 | 0.40 | 0.77 | 19 | empty |
| 4 | 157 | 0.40 | 0.73 | 34 | empty |
| 5 | 58 | 0.40 | 0.80 | 12 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 1514 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1055 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 992 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3P9W · Crystal structure of an engineered human autonomous VH Domain in complex with VEGF · the same entry in another collection · chain A against A, 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 3P9W · PDBe 3P9W · UniProt P15692
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