MolNFT v1 · #148687 · protein
Structure of chlamydia trachomatis effector protein CDU1 bound to compound 3
6FDU · Deubiquitinase and deneddylase DUB1: “Structure of chlamydia trachomatis effector protein CDU1 bound to compound 3”. X-ray diffraction, 2 ligands (D5W, CL), 8 pockets (best druggability 0.68). MolNFT v1 #148687 on GenesisL1: 3D…
- PDB
- 6FDU
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deubiquitinase and deneddylase DUB1
- EC
- 3.4.22.-
- UniProt
- B0B9A0
- Ligands
- D5W, CL
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deubiquitinase and deneddylase DUB1 (EC 3.4.22.-) | protein | 240 | 43% helix, 11% strand | B0B9A0 |
| B | Deubiquitinase and deneddylase DUB1 (EC 3.4.22.-) | protein | 239 | 43% helix, 11% strand | B0B9A0 |
Ligands and binding sites
- D5W · (2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.68 | 0.78 | 63 | D5W |
| 2 | 130 | 0.51 | 0.80 | 20 | empty |
| 3 | 150 | 0.50 | 0.79 | 18 | empty |
| 4 | 146 | 0.50 | 0.79 | 24 | empty |
| 5 | 132 | 0.42 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6FDU · Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3 · 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 6FDU · PDBe 6FDU · UniProt B0B9A0
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