MolNFT v1 · #12477 · protein
The crystal structure of clpb N terminal domain, implication to the peptide binding function of clpb
1KHY · Clpb protein: “The crystal structure of clpb N terminal domain, implication to the peptide binding function of clpb”. X-ray diffraction, 4 pockets (best druggability 0.71). MolNFT v1 #12477 on GenesisL1: 3D structure, binding sites…
- PDB
- 1KHY
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clpb protein
- UniProt
- P63284
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clpb protein | protein | 132 | 67% helix, 3% strand | P63284 |
| B | Clpb protein | protein | 133 | 68% helix, 3% strand | P63284 |
| C | Clpb protein | protein | 135 | 67% helix, 4% strand | P63284 |
| D | Clpb protein | protein | 140 | 63% helix, 6% strand | P63284 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.71 | 0.75 | 80 | empty |
| 2 | 165 | 0.50 | 0.78 | 24 | empty |
| 3 | 66 | 0.38 | 0.79 | 16 | empty |
| 4 | 57 | 0.32 | 0.76 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–D · 420 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1KHY · The Crystal Structure of ClpB N Terminal Domain, Implication to the Peptide Binding… · the same entry in another collection · chain B against B, TM-score 1.00
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 1KHY · PDBe 1KHY · UniProt P63284
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