MolNFT v1 · #178822 · protein
Structure of the hazara virus otu bound to ubiquitin
7JMS · Replicase: “Structure of the hazara virus otu bound to ubiquitin”. X-ray diffraction, 2 ligands (AYE, CA), 11 pockets (best druggability 0.64). MolNFT v1 #178822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JMS
- Type
- protein
- Length
- 931 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase; Polyubiquitin-B
- EC
- 2.7.7.48, 3.4.19.12
- UniProt
- A6XA53, P0CG47
- Ligands
- AYE, CA
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Replicase (EC 2.7.7.48, 3.4.19.12) | protein | 157 | 38% helix, 25% strand | A6XA53 |
| B, D, F, H | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | P0CG47 |
| C | Replicase (EC 2.7.7.48, 3.4.19.12) | protein | 159 | 37% helix, 25% strand | A6XA53 |
| E | Replicase (EC 2.7.7.48, 3.4.19.12) | protein | 158 | 35% helix, 23% strand | A6XA53 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · 2 copies · chains B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.64 | 0.77 | 46 | empty |
| 2 | 359 | 0.56 | 0.75 | 42 | CA |
| 3 | 206 | 0.47 | 0.74 | 23 | empty |
| 4 | 119 | 0.43 | 0.77 | 24 | empty |
| 5 | 103 | 0.40 | 0.76 | 17 | empty |
Interfaces
10 interfaces between chains.
- G–H · 971 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 962 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 940 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 919 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 471 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7JMS · Structure of the Hazara virus OTU bound to ubiquitin · 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 A6XA53
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7JMS · PDBe 7JMS · UniProt A6XA53 · UniProt P0CG47
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