MolNFT v1 · #129285 · protein
Cryo EM structure of the E. COLI disaggregase clpb (bap form, dwb mutant), in the atpgammas state, bound to the model substrate casein
5OFO · Chaperone protein CLPB,ATP-dependent clp protease ATP…: “Cryo EM structure of the E. COLI disaggregase clpb (bap form, dwb mutant), in the atpgammas state, bound to…”. Electron microscopy, 1 ligand (AGS), 20 pockets (best…
- 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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