MolNFT v1 · #168137 · protein
The mycobacterium tuberculosis clpb disaggregase hexamer structure with a locally refined N-terminal domain in the presence of dnak chaperone and a model substrate
6W6J · Chaperone protein clpb: “The mycobacterium tuberculosis clpb disaggregase hexamer structure with a locally refined N-terminal domain…”. Electron microscopy, 2 ligands (AGS, ADP), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6W6J
- Type
- protein
- Length
- 3,751 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Substrate
- UniProt
- P9WPD0
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein clpb | protein | 620 | 47% helix, 10% strand | P9WPD0 |
| B | Chaperone protein clpb | protein | 621 | 45% helix, 11% strand | P9WPD0 |
| C | Chaperone protein clpb | protein | 624 | 47% helix, 10% strand | P9WPD0 |
| D | Chaperone protein clpb | protein | 707 | 46% helix, 9% strand | P9WPD0 |
| E | Chaperone protein clpb | protein | 548 | 39% helix, 7% strand | P9WPD0 |
| F | Chaperone protein clpb | protein | 605 | 45% helix, 8% strand | P9WPD0 |
| N | Substrate | protein | 26 | 0% helix, 12% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 10 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.86 | 0.88 | 104 | AGS |
| 2 | 719 | 0.83 | 0.87 | 87 | AGS |
| 3 | 1071 | 0.83 | 0.84 | 79 | AGS |
| 4 | 1038 | 0.83 | 0.84 | 88 | AGS |
| 5 | 1163 | 0.82 | 0.84 | 113 | AGS |
Interfaces
17 interfaces between chains.
- B–C · 4649 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 4646 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4544 Ų buried · 59 hydrogen bonds · protein-protein
- A–F · 3509 Ų buried · 50 hydrogen bonds · protein-protein
- D–E · 2140 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 6W6J · The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally refined… · the same entry in another collection · chain N against N, TM-score 1.00
- P9WPD0 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P9WPD0) · a predicted model of the same protein · chain E against A, TM-score 0.78
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 P9WPD0
- Elsewhere: RCSB PDB 6W6J · PDBe 6W6J · UniProt P9WPD0
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