Research workbench
Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin
Analyse Structure of Chlamydia trachomatis effector protein ChlaDUB1 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
- 6GZS
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B); Homo sapiens
- Molecule
- Deubiquitinase and deneddylase Dub1; Polyubiquitin-B
- EC
- 3.4.22.-
- UniProt
- B0B9A0, P0CG47
- Ligands
- AYE, SO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deubiquitinase and deneddylase Dub1 (EC 3.4.22.-) | protein | 250 | 48% helix, 11% strand | B0B9A0 |
| B | Polyubiquitin-B | protein | 75 | 24% helix, 29% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.67 | 0.91 | 30 | empty |
| 2 | 274 | 0.64 | 0.81 | 29 | empty |
| 3 | 57 | 0.41 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6GZS · Structure of chlamydia trachomatis effector protein CHLADUB1 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 0.99
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 6GZS · PDBe 6GZS · UniProt B0B9A0 · UniProt P0CG47
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