Research workbench
Structure of chlamydia trachomatis effector protein CDU1 bound to ubiquitin
Analyse Structure of chlamydia trachomatis effector protein CDU1 bound to ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FDK
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deubiquitinase and deneddylase DUB1; Polyubiquitin-B
- EC
- 3.4.22.-
- UniProt
- B0B9A0, P0CG47
- Ligands
- AYE, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deubiquitinase and deneddylase DUB1 (EC 3.4.22.-) | protein | 242 | 45% helix, 12% strand | B0B9A0 |
| B | Polyubiquitin-B | protein | 75 | 25% helix, 32% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.67 | 0.81 | 36 | empty |
| 2 | 55 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6FDK · Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- B0B9A0 · AlphaFold monomer V2.0 prediction for deubiquitinase and deneddylase DUB1 (B0B9A0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B0B9A0
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6FDK · PDBe 6FDK · UniProt B0B9A0 · UniProt P0CG47
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