Research workbench
Cryo EM structure of the E. COLI disaggregase clpb (bap form, dwb mutant), in the atpgammas state, bound to the model substrate casein
Analyse Cryo EM structure of the E. COLI disaggregase clpb (bap form, dwb mutant), in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OFO
- Type
- protein
- Length
- 4,116 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE…
- UniProt
- P63284, P0ABH9
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, F, E, D, B, A | Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE protein clpb | protein | 686 | 56% helix, 10% strand | P63284, P0ABH9 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 11 copies · chains C, B, F, E, D, 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 | 1170 | 0.83 | 0.84 | 118 | empty |
| 2 | 1030 | 0.83 | 0.84 | 82 | AGS |
| 3 | 897 | 0.83 | 0.85 | 89 | AGS |
| 4 | 806 | 0.83 | 0.86 | 77 | AGS |
| 5 | 552 | 0.83 | 0.88 | 64 | AGS |
Interfaces
9 interfaces between chains.
- C–D · 4220 Ų buried · 72 hydrogen bonds · protein-protein
- C–B · 4120 Ų buried · 58 hydrogen bonds · protein-protein
- E–D · 3896 Ų buried · 60 hydrogen bonds · protein-protein
- B–A · 3273 Ų buried · 49 hydrogen bonds · protein-protein
- F–E · 2363 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5OFO · Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the… · the same entry in another collection · chain C against C, TM-score 1.00
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain A against A, TM-score 0.81
- P0ABH9 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.70
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
- Every structure of UniProt P0ABH9
- Elsewhere: RCSB PDB 5OFO · PDBe 5OFO · UniProt P63284 · UniProt P0ABH9
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