MolNFT v1 · #168235 · protein
Crystal structure of an otu deubiquitinase from wolbachia pipientis wmel bound to ubiquitin
6W9R: “Crystal structure of an otu deubiquitinase from wolbachia pipientis wmel bound to ubiquitin”. X-ray diffraction, 1 ligand (NEH), 20 pockets (best druggability 0.78). MolNFT v1 #168235 on GenesisL1: 3D structure, binding sites and…
- 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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