Research workbench
Clpb (dwb mutant) bound to casein in presence of atpgammas - state wt- 1
Analyse Clpb (dwb mutant) bound to casein in presence of atpgammas - state wt- 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RN2
- Type
- protein
- Length
- 4,138 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Casein
- UniProt
- V2RJ62
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Chaperone protein clpb | protein | 684 | 58% helix, 9% strand | V2RJ62 |
| B, C | Chaperone protein clpb | protein | 689 | 57% helix, 10% strand | V2RJ62 |
| S | Casein | protein | 24 | 0% helix, 13% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 9 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, E, F
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 | 615 | 0.86 | 0.91 | 107 | empty |
| 2 | 1111 | 0.85 | 0.86 | 100 | empty |
| 3 | 587 | 0.84 | 0.89 | 83 | AGS |
| 4 | 837 | 0.83 | 0.86 | 68 | empty |
| 5 | 821 | 0.83 | 0.86 | 81 | AGS |
Interfaces
16 interfaces between chains.
- B–C · 4702 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 4548 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4170 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 3537 Ų buried · 45 hydrogen bonds · protein-protein
- A–F · 2526 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 covalent (covalent ligand).
Compared structures
- 6RN2 · ClpB (DWB mutant) bound to casein in presence of ATPgammaS - state WT-1 · the same entry in another collection · chain A against A, 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
- Every structure of UniProt V2RJ62
- Elsewhere: RCSB PDB 6RN2 · PDBe 6RN2 · UniProt V2RJ62
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