MolNFT v1 · #119402 · protein
Crystal structure of hvegf in complex with vk domain antibody
5FV1: “Crystal structure of hvegf in complex with vk domain antibody”. X-ray diffraction, 5 pockets (best druggability 0.50). MolNFT v1 #119402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FV1
- Type
- protein
- Length
- 410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vk domain antibody; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Vk domain antibody | protein | 108 | 3% helix, 48% strand | — |
| M | Vk domain antibody | protein | 107 | 3% helix, 48% strand | — |
| V | Vascular endothelial growth factor a | protein | 95 | 11% helix, 63% strand | P15692 |
| W | Vascular endothelial growth factor a | protein | 100 | 12% helix, 60% strand | P15692 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.50 | 0.74 | 40 | empty |
| 2 | 137 | 0.42 | 0.75 | 22 | empty |
| 3 | 124 | 0.35 | 0.72 | 33 | empty |
| 4 | 69 | 0.30 | 0.73 | 17 | empty |
| 5 | 60 | 0.29 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1346 Ų buried · 12 hydrogen bonds · protein-protein
- M–W · 410 Ų buried · 2 hydrogen bonds · protein-protein
- L–V · 406 Ų buried · 2 hydrogen bonds · protein-protein
- L–W · 257 Ų buried · 6 hydrogen bonds · protein-protein
- M–V · 193 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5FV1 · Crystal structure of hVEGF in complex with VK domain antibody · the same entry in another collection · chain L against L, 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 5FV1 · PDBe 5FV1 · UniProt P15692
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