MolNFT v1 · #162912 · protein
Clpb (dwb mutant) bound to casein in presence of atpgammas - state wt- 2A
6RN3 · Chaperone protein clpb: “Clpb (dwb mutant) bound to casein in presence of atpgammas - state wt- 2A”. Electron microscopy, 2 ligands (AGS, ADP), 20 pockets (best druggability 0.84). MolNFT v1 #162912 on GenesisL1: 3D structure…
- PDB
- 6RN3
- Type
- protein
- Length
- 4,129 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 0.84
Structure
electron microscopy · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Chaperone protein clpb | protein | 684 | 56% helix, 9% strand | V2RJ62 |
| B, C | Chaperone protein clpb | protein | 689 | 55% helix, 10% strand | V2RJ62 |
| F | Chaperone protein clpb | protein | 675 | 53% helix, 10% strand | V2RJ62 |
| S | Casein | protein | 24 | 0% helix, 8% 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 | 406 | 0.84 | 0.93 | 59 | AGS |
| 2 | 493 | 0.83 | 0.90 | 62 | AGS |
| 3 | 1024 | 0.83 | 0.84 | 95 | AGS |
| 4 | 719 | 0.83 | 0.86 | 70 | ADP |
| 5 | 1024 | 0.83 | 0.84 | 86 | AGS |
Interfaces
17 interfaces between chains.
- B–C · 4512 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 4468 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 4168 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4060 Ų buried · 71 hydrogen bonds · protein-protein
- E–F · 3048 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 covalent (covalent ligand).
Compared structures
- 6RN3 · ClpB (DWB mutant) bound to casein in presence of ATPgammaS - state WT-2A · the same entry in another collection · chain E against E, 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 6RN3 · PDBe 6RN3 · UniProt V2RJ62
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