Research workbench
Structure of chlamydia trachomatis effector protein CHLADUB1 bound to coenzyme a
Analyse Structure of chlamydia trachomatis effector protein CHLADUB1 bound to coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GZT
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deubiquitinase and deneddylase DUB1
- EC
- 3.4.22.-
- UniProt
- B0B9A0
- Ligands
- COA, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deubiquitinase and deneddylase DUB1 (EC 3.4.22.-) | protein | 267 | 46% helix, 10% strand | B0B9A0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.63 | 0.87 | 22 | GOL |
| 2 | 103 | 0.48 | 0.80 | 22 | GOL |
| 3 | 53 | 0.39 | 0.81 | 14 | GOL |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6GZT · Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to Coenzyme A · 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
- Elsewhere: RCSB PDB 6GZT · PDBe 6GZT · UniProt B0B9A0
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