Research workbench
The mycobacterium tuberculosis clpb disaggregase hexamer structure with a locally refined clpb middle domain and a dnak nucleotide binding domain
Analyse The mycobacterium tuberculosis clpb disaggregase hexamer structure with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W6E
- Type
- protein
- Length
- 3,958 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Chaperone protein dnak; Substrate
- UniProt
- P9WPD0, A0A045JRR0
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein clpb | protein | 674 | 50% helix, 8% strand | P9WPD0 |
| B | Chaperone protein clpb | protein | 621 | 45% helix, 11% strand | P9WPD0 |
| C | Chaperone protein clpb | protein | 624 | 48% helix, 8% strand | P9WPD0 |
| D | Chaperone protein clpb | protein | 562 | 43% helix, 9% strand | P9WPD0 |
| E | Chaperone protein clpb | protein | 548 | 40% helix, 7% strand | P9WPD0 |
| F | Chaperone protein clpb | protein | 546 | 40% helix, 9% strand | P9WPD0 |
| I | Chaperone protein dnak | protein | 357 | 42% helix, 27% strand | A0A045JRR0 |
| 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 | 1173 | 0.85 | 0.86 | 121 | AGS |
| 2 | 952 | 0.84 | 0.85 | 107 | empty |
| 3 | 1103 | 0.83 | 0.84 | 93 | AGS |
| 4 | 943 | 0.83 | 0.84 | 69 | AGS |
| 5 | 771 | 0.82 | 0.85 | 73 | empty |
Interfaces
17 interfaces between chains.
- B–C · 4735 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 4669 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4655 Ų buried · 69 hydrogen bonds · protein-protein
- A–F · 2946 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2264 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6W6E · 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 0.79
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
- Every structure of UniProt A0A045JRR0
- Elsewhere: RCSB PDB 6W6E · PDBe 6W6E · UniProt P9WPD0 · UniProt A0A045JRR0
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