MolNFT v1 · #129298 · protein
Cryo EM structure of the E. COLI disaggregase clpb (bap form, dwb mutant), in the atpgammas state
5OG1 · 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”. Electron microscopy, 1 ligand (AGS), 20 pockets (best druggability 0.88).…
- PDB
- 5OG1
- Type
- protein
- Length
- 4,011 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 0.88
Structure
electron microscopy · 4 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE protein clpb | protein | 624 | 47% helix, 8% strand | P63284, P0ABH9 |
| F, E | Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE protein clpb | protein | 686 | 56% helix, 8% strand | P63284, P0ABH9 |
| B | Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE protein clpb | protein | 572 | 46% helix, 9% strand | P63284, P0ABH9 |
| A | Chaperone protein CLPB,ATP-dependent clp protease ATP- binding subunit CLPA,CHAPERONE protein clpb | protein | 819 | 47% helix, 7% strand | P63284, P0ABH9 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 7 copies · chains C, B, 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 | 984 | 0.88 | 0.89 | 142 | empty |
| 2 | 1037 | 0.86 | 0.87 | 108 | AGS |
| 3 | 808 | 0.85 | 0.87 | 103 | empty |
| 4 | 702 | 0.84 | 0.88 | 114 | empty |
| 5 | 702 | 0.84 | 0.88 | 79 | AGS |
Interfaces
10 interfaces between chains.
- C–D · 4298 Ų buried · 59 hydrogen bonds · protein-protein
- C–B · 4225 Ų buried · 57 hydrogen bonds · protein-protein
- E–D · 3085 Ų buried · 44 hydrogen bonds · protein-protein
- F–E · 2998 Ų buried · 57 hydrogen bonds · protein-protein
- F–A · 2438 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5OG1 · Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the… · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.81
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain F against A, TM-score 0.76
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 5OG1 · PDBe 5OG1 · UniProt P63284 · UniProt P0ABH9
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