Research workbench
Crystal structure of human cardiovirus safv-3
Analyse Crystal structure of human cardiovirus safv-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CFC
- 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, E3TMG8, C5J497
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 9% 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, 34% strand | E3TMG8 |
| C | VP2 | protein | 258 | 12% helix, 37% strand | C0MHL9 |
| D | VP4 | protein | 24 | 17% helix, 8% strand | C5J497 |
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.65 | 0.94 | 15 | empty |
| 2 | 251 | 0.58 | 0.78 | 30 | empty |
| 3 | 151 | 0.50 | 0.78 | 22 | empty |
| 4 | 59 | 0.50 | 0.86 | 15 | empty |
| 5 | 125 | 0.48 | 0.79 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3516 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 2141 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1610 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 720 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 400 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CFC · Crystal Structure of 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
- Every structure of UniProt E3TMG8
- Every structure of UniProt C5J497
- Elsewhere: RCSB PDB 5CFC · PDBe 5CFC · UniProt C0MHL9 · UniProt E3TMG8 · UniProt C5J497
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