MolNFT v1 · #69725 · protein
Crystal structure of the rotavirus double layered particle
3KZ4 · Inner capsid protein VP2: “Crystal structure of the rotavirus double layered particle”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #69725 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3KZ4
- Type
- protein
- Length
- 6,752 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner capsid protein VP2; Intermediate capsid protein VP6
- UniProt
- A7J3A1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner capsid protein VP2 | protein | 781 | 41% helix, 9% strand | — |
| B | Inner capsid protein VP2 | protein | 810 | 41% helix, 9% strand | — |
| C, D, E, F, G, H, I, J, K, L, M, N, O | Intermediate capsid protein VP6 | protein | 397 | 29% helix, 32% strand | A7J3A1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.87 | 0.94 | 85 | empty |
| 2 | 530 | 0.87 | 0.93 | 91 | empty |
| 3 | 1029 | 0.87 | 0.88 | 131 | empty |
| 4 | 1072 | 0.87 | 0.88 | 119 | empty |
| 5 | 511 | 0.86 | 0.93 | 85 | empty |
Interfaces
39 interfaces between chains.
- I–K · 2630 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2621 Ų buried · 37 hydrogen bonds · protein-protein
- L–M · 2609 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2609 Ų buried · 37 hydrogen bonds · protein-protein
- L–N · 2603 Ų buried · 40 hydrogen bonds · protein-protein
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 A7J3A1
- Elsewhere: RCSB PDB 3KZ4 · PDBe 3KZ4 · UniProt A7J3A1
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