Research workbench
The mycobacterium tuberculosis clpb disaggregase hexamer structure with three locally refined clpb middle domains and three dnak nucleotide binding domains
Analyse The mycobacterium tuberculosis clpb disaggregase hexamer structure with three… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L6N
- Type
- protein
- Length
- 4,774 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Substrate; Chaperone protein dnak
- UniProt
- P9WPD0, A0A045JRR0
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 45% helix, 10% 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 | 672 | 49% helix, 10% strand | P9WPD0 |
| C | Chaperone protein clpb | protein | 675 | 50% 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 |
| N | Substrate | protein | 26 | 0% helix, 12% strand | — |
| I, J, K | Chaperone protein dnak | protein | 357 | 41% helix, 26% strand | A0A045JRR0 |
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 | 1183 | 0.85 | 0.86 | 123 | AGS |
| 2 | 927 | 0.84 | 0.85 | 104 | empty |
| 3 | 826 | 0.83 | 0.86 | 69 | AGS |
| 4 | 1106 | 0.83 | 0.84 | 93 | AGS |
| 5 | 769 | 0.82 | 0.85 | 73 | empty |
Interfaces
19 interfaces between chains.
- B–C · 4738 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 4668 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4653 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: 3 covalent (covalent ligand).
Compared structures
- 7L6N · The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with three locally… · the same entry in another collection · chain K against K, 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 7L6N · PDBe 7L6N · UniProt P9WPD0 · UniProt A0A045JRR0
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