MolNFT v1 · #115297 · protein
Crystal structure of dtt treated human cardiovirus safv-3
5CFD · VP1: “Crystal structure of dtt treated human cardiovirus safv-3”. X-ray diffraction, 10 pockets (best druggability 0.65). MolNFT v1 #115297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CFD
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP3; VP2; VP4
- UniProt
- C0MHL9
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 252 | 6% helix, 34% strand | C0MHL9 |
| B | VP3 | protein | 232 | 7% helix, 33% strand | C0MHL9 |
| C | VP2 | protein | 258 | 14% helix, 37% strand | C0MHL9 |
| D | VP4 | protein | 24 | 17% helix, 8% strand | C0MHL9 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.65 | 0.94 | 15 | empty |
| 2 | 271 | 0.59 | 0.78 | 28 | empty |
| 3 | 64 | 0.52 | 0.87 | 17 | empty |
| 4 | 155 | 0.50 | 0.78 | 24 | empty |
| 5 | 116 | 0.48 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3528 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2151 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1590 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 745 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5CFD · Crystal Structure of DTT treated Human Cardiovirus SAFV-3 · 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 C0MHL9
- Elsewhere: RCSB PDB 5CFD · PDBe 5CFD · UniProt C0MHL9
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