MolNFT v1 · #152460 · protein
Cryoem structure of mud crab dicistrovirus
6IIC · VP1 of mud crab dicistrovirus: “Cryoem structure of mud crab dicistrovirus”. Electron microscopy, 12 pockets (best druggability 0.56). MolNFT v1 #152460 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IIC
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 of mud crab dicistrovirus; VP2 of mud crab dicistrovirus; VP3 of mud crab…
- UniProt
- E5G7H9
- Pockets
- 12 · best druggability 0.56
Structure
electron microscopy · 4 distinct chains · 12% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 of mud crab dicistrovirus | protein | 188 | 10% helix, 28% strand | E5G7H9 |
| B | VP2 of mud crab dicistrovirus | protein | 250 | 12% helix, 32% strand | E5G7H9 |
| C | VP3 of mud crab dicistrovirus | protein | 253 | 6% helix, 29% strand | E5G7H9 |
| D | VP4 of mud crab dicistrovirus | protein | 56 | 38% helix, 7% strand | E5G7H9 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.56 | 0.80 | 34 | empty |
| 2 | 180 | 0.53 | 0.79 | 32 | empty |
| 3 | 123 | 0.52 | 0.81 | 29 | empty |
| 4 | 189 | 0.49 | 0.76 | 27 | empty |
| 5 | 87 | 0.47 | 0.82 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3699 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1457 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 126 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IIC · CryoEM structure of Mud Crab Dicistrovirus · 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 E5G7H9
- Elsewhere: RCSB PDB 6IIC · PDBe 6IIC · UniProt E5G7H9
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