Research workbench
Crystal structure of an otu deubiquitinase from wolbachia pipientis wmel bound to ubiquitin
Analyse Crystal structure of an otu deubiquitinase from wolbachia pipientis wmel bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W9R
- Type
- protein
- Length
- 2,846 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Otu domain-containing protein wmelotu
- UniProt
- P0CG48, Q73HU7
- Ligands
- NEH
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N, O, P, Q, R, S, T, U, V, W, X | Ubiquitin | protein | 75 | 24% helix, 35% strand | P0CG48 |
| A, E, H | Otu domain-containing protein wmelotu | protein | 162 | 33% helix, 26% strand | Q73HU7 |
| B, C, J, L | Otu domain-containing protein wmelotu | protein | 163 | 34% helix, 26% strand | Q73HU7 |
| D | Otu domain-containing protein wmelotu | protein | 162 | 33% helix, 26% strand | Q73HU7 |
| F, I, K | Otu domain-containing protein wmelotu | protein | 161 | 33% helix, 26% strand | Q73HU7 |
| G | Otu domain-containing protein wmelotu | protein | 163 | 33% helix, 27% strand | Q73HU7 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 12 copies · chains M, A, N, B, O, F, P, D, Q, I, R, J, S, E, T, C, U, K, V, L, W, G, X, H
- FLC · Citrate anion · additive · 12 copies · chains M, A, N, B, O, F, P, D, Q, I, R, J, S, E, T, C, U, G, K, V, H, L, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.78 | 0.82 | 80 | empty |
| 2 | 1009 | 0.77 | 0.79 | 84 | FLC |
| 3 | 583 | 0.75 | 0.83 | 80 | NEH |
| 4 | 969 | 0.75 | 0.78 | 78 | FLC |
| 5 | 557 | 0.75 | 0.83 | 81 | NEH |
Interfaces
49 interfaces between chains.
- M–A · 1535 Ų buried · 35 hydrogen bonds · protein-protein
- T–C · 1532 Ų buried · 38 hydrogen bonds · protein-protein
- U–K · 1523 Ų buried · 29 hydrogen bonds · protein-protein
- S–E · 1521 Ų buried · 40 hydrogen bonds · protein-protein
- V–L · 1517 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 covalent (covalent ligand).
Compared structures
- 6W9R · Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to… · the same entry in another collection · chain Q against Q, 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 P0CG48
- Every structure of UniProt Q73HU7
- Elsewhere: RCSB PDB 6W9R · PDBe 6W9R · UniProt P0CG48 · UniProt Q73HU7
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