Research workbench
Structure of the hyperactive clpb mutant K476C, bound to casein, pre- state
Analyse Structure of the hyperactive clpb mutant K476C, bound to casein, pre- state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OAX
- Type
- protein
- Length
- 3,500 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyperactive disaggregase clpb; Alpha-S1-casein
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, B, A | Hyperactive disaggregase clpb | protein | 581 | 42% helix, 14% strand | — |
| F | Hyperactive disaggregase clpb | protein | 571 | 27% helix, 4% strand | — |
| E | Hyperactive disaggregase clpb | protein | 579 | 44% helix, 9% strand | — |
| P | Alpha-S1-casein | protein | 26 | 0% helix, 23% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 9 copies · chains C, B, E, D, A, F
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains F, E, A
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 | 1040 | 0.87 | 0.89 | 124 | empty |
| 2 | 1114 | 0.84 | 0.85 | 128 | empty |
| 3 | 966 | 0.83 | 0.85 | 88 | AGS |
| 4 | 760 | 0.83 | 0.86 | 91 | empty |
| 5 | 727 | 0.82 | 0.86 | 94 | empty |
Interfaces
15 interfaces between chains.
- E–D · 4572 Ų buried · 84 hydrogen bonds · protein-protein
- C–B · 4542 Ų buried · 87 hydrogen bonds · protein-protein
- C–D · 4405 Ų buried · 87 hydrogen bonds · protein-protein
- B–A · 4362 Ų buried · 87 hydrogen bonds · protein-protein
- F–E · 2247 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6OAX · Structure of the hyperactive ClpB mutant K476C, bound to casein, pre-state · the same entry in another collection · chain P against P, 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
- Elsewhere: RCSB PDB 6OAX · PDBe 6OAX
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