Research workbench
Two-step activation mechanism of the clpb disaggregase for sequential substrate threading by the main ATPase motor.
Analyse Two-step activation mechanism of the clpb disaggregase for sequential substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QS4
- Type
- protein
- Length
- 3,622 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Casein
- UniProt
- E0J719
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Chaperone protein clpb | protein | 568 | 49% helix, 11% strand | E0J719 |
| B | Chaperone protein clpb | protein | 582 | 50% helix, 11% strand | E0J719 |
| C | Chaperone protein clpb | protein | 630 | 51% helix, 11% strand | E0J719 |
| D, E | Chaperone protein clpb | protein | 625 | 51% helix, 11% strand | E0J719 |
| S | Casein | protein | 24 | 0% helix, 8% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 9 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, 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 | 777 | 0.85 | 0.88 | 82 | AGS |
| 2 | 1074 | 0.84 | 0.85 | 120 | AGS |
| 3 | 524 | 0.84 | 0.90 | 76 | AGS |
| 4 | 973 | 0.83 | 0.85 | 87 | ADP |
| 5 | 679 | 0.83 | 0.88 | 99 | empty |
Interfaces
16 interfaces between chains.
- C–D · 4960 Ų buried · 84 hydrogen bonds · protein-protein
- D–E · 4756 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 4729 Ų buried · 71 hydrogen bonds · protein-protein
- E–F · 3196 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3057 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 6QS4 · Two-Step Activation Mechanism of the ClpB Disaggregase for Sequential Substrate Threading… · the same entry in another collection · chain A against A, TM-score 1.00
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 E0J719
- Elsewhere: RCSB PDB 6QS4 · PDBe 6QS4 · UniProt E0J719
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