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Cryo-EM structure of B. subtilis clpc (dwb mutant) hexamer bound to a substrate polypeptide
Analyse Cryo-EM structure of B. subtilis clpc (dwb mutant) hexamer bound to a substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ABR
- Type
- protein
- Length
- 3,445 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Negative regulator of genetic competence CLPC/MECB; Substrate polypeptide
- UniProt
- P37571
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Negative regulator of genetic competence CLPC/MECB | protein | 574 | 49% helix, 11% strand | P37571 |
| B | Negative regulator of genetic competence CLPC/MECB | protein | 574 | 49% helix, 12% strand | P37571 |
| C | Negative regulator of genetic competence CLPC/MECB | protein | 578 | 50% helix, 11% strand | P37571 |
| D | Negative regulator of genetic competence CLPC/MECB | protein | 586 | 51% helix, 12% strand | P37571 |
| E | Negative regulator of genetic competence CLPC/MECB | protein | 571 | 48% helix, 12% strand | P37571 |
| F | Negative regulator of genetic competence CLPC/MECB | protein | 536 | 52% helix, 11% strand | P37571 |
| S | Substrate polypeptide | protein | 26 | 0% helix, 23% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, F, B, E
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 | 1153 | 0.86 | 0.87 | 131 | ATP |
| 2 | 1012 | 0.85 | 0.86 | 103 | empty |
| 3 | 666 | 0.85 | 0.89 | 66 | ATP |
| 4 | 913 | 0.84 | 0.86 | 91 | ATP |
| 5 | 801 | 0.83 | 0.86 | 89 | ATP |
Interfaces
15 interfaces between chains.
- C–D · 4316 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 4164 Ų buried · 61 hydrogen bonds · protein-protein
- D–E · 4045 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3354 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2137 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 7ABR · Cryo-EM structure of B. subtilis ClpC (DWB mutant) hexamer bound to a substrate… · the same entry in another collection · chain S against S, TM-score 1.00
- P37571 · AlphaFold monomer V2.0 prediction for negative regulator of genetic competence CLPC/MECB… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P37571
- Elsewhere: RCSB PDB 7ABR · PDBe 7ABR · UniProt P37571
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