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Crystal structure of an engineered human autonomous vh domain in complex with VEGF
Analyse Crystal structure of an engineered human autonomous vh domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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