Research workbench
Crystal structure of a bacterial otu dub with ub-pa
Analyse Crystal structure of a bacterial otu dub with ub-pa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W54
- Type
- protein
- Length
- 1,325 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LPG2248; Polyubiquitin-B
- UniProt
- Q5ZTB4, J3QS39
- Ligands
- AYE
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LPG2248 | protein | 513 | 53% helix, 8% strand | Q5ZTB4 |
| B | LPG2248 | protein | 518 | 53% helix, 8% strand | Q5ZTB4 |
| C, E | Polyubiquitin-B | protein | 75 | 23% helix, 36% strand | J3QS39 |
| D | Polyubiquitin-B | protein | 73 | 21% helix, 32% strand | J3QS39 |
| F | Polyubiquitin-B | protein | 71 | 21% helix, 34% strand | J3QS39 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, C, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.84 | 0.87 | 98 | empty |
| 2 | 997 | 0.79 | 0.81 | 81 | empty |
| 3 | 655 | 0.76 | 0.82 | 75 | empty |
| 4 | 182 | 0.71 | 0.89 | 25 | empty |
| 5 | 195 | 0.68 | 0.86 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3220 Ų buried · 53 hydrogen bonds · protein-protein
- B–E · 1245 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1166 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 991 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 969 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 7W54 · Crystal structure of a bacterial OTU DUB with Ub-PA · the same entry in another collection · chain E against E, 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 Q5ZTB4
- Every structure of UniProt J3QS39
- Elsewhere: RCSB PDB 7W54 · PDBe 7W54 · UniProt Q5ZTB4 · UniProt J3QS39
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