Research workbench
Clpb (dwb and K476C mutant) bound to casein in presence of atpgammas - state kc-1
Analyse Clpb (dwb and K476C mutant) bound to casein in presence of atpgammas - state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QS6
- Type
- protein
- Length
- 3,592 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Casein
- UniProt
- P63284
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Chaperone protein clpb | protein | 577 | 50% helix, 13% strand | P63284 |
| B | Chaperone protein clpb | protein | 582 | 51% helix, 12% strand | P63284 |
| C | Chaperone protein clpb | protein | 630 | 52% helix, 11% strand | P63284 |
| D | Chaperone protein clpb | protein | 625 | 53% helix, 11% strand | P63284 |
| S | Casein | protein | 24 | 0% helix, 17% 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 A, 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 | 1082 | 0.84 | 0.85 | 101 | AGS |
| 2 | 985 | 0.84 | 0.85 | 121 | empty |
| 3 | 808 | 0.84 | 0.86 | 66 | AGS |
| 4 | 973 | 0.83 | 0.84 | 87 | ADP |
| 5 | 563 | 0.83 | 0.88 | 72 | AGS |
Interfaces
16 interfaces between chains.
- C–D · 4830 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 4762 Ų buried · 88 hydrogen bonds · protein-protein
- A–B · 3921 Ų buried · 68 hydrogen bonds · protein-protein
- D–E · 3718 Ų buried · 61 hydrogen bonds · protein-protein
- E–F · 2539 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 covalent (covalent ligand).
Compared structures
- 6QS6 · ClpB (DWB and K476C mutant) bound to casein in presence of ATPgammaS - state KC-1 · the same entry in another collection · chain S against S, TM-score 1.00
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain F 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 P63284
- Elsewhere: RCSB PDB 6QS6 · PDBe 6QS6 · UniProt P63284
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