Research workbench
Crystal structure of hvegf in complex with vh domain antibody
Analyse Crystal structure of hvegf in complex with vh domain antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FV2
- Type
- protein
- Length
- 637 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vh domain antibody; Vascular endothelial growth factor
- UniProt
- P15692
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vh domain antibody | protein | 116 | 3% helix, 48% strand | — |
| B | Vh domain antibody | protein | 115 | 5% helix, 50% strand | — |
| V | Vascular endothelial growth factor | protein | 96 | 11% helix, 60% strand | P15692 |
| W, X | Vascular endothelial growth factor | protein | 97 | 12% helix, 61% strand | P15692 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.60 | 0.78 | 34 | empty |
| 2 | 221 | 0.52 | 0.76 | 37 | empty |
| 3 | 178 | 0.49 | 0.77 | 34 | empty |
| 4 | 171 | 0.44 | 0.74 | 28 | empty |
| 5 | 119 | 0.37 | 0.74 | 26 | empty |
Interfaces
9 interfaces between chains.
- V–W · 1376 Ų buried · 7 hydrogen bonds · protein-protein
- A–X · 683 Ų buried · 6 hydrogen bonds · protein-protein
- C–W · 670 Ų buried · 6 hydrogen bonds · protein-protein
- B–V · 644 Ų buried · 3 hydrogen bonds · protein-protein
- A–V · 447 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5FV2 · Crystal structure of hVEGF in complex with VH domain antibody · 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 5FV2 · PDBe 5FV2 · UniProt P15692
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