Research workbench
Clpb NBD2 R621Q from T. thermophilus in complex with amppcp and guanidinium chloride
Analyse Clpb NBD2 R621Q from T. thermophilus in complex with amppcp and guanidinium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LJA
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb
- UniProt
- Q9RA63
- Ligands
- ACP, GAI, MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein clpb | protein | 321 | 51% helix, 15% strand | Q9RA63 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- GAI · Guanidine · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.57 | 0.78 | 28 | ACP, MG, GAI |
| 2 | 161 | 0.50 | 0.78 | 18 | empty |
| 3 | 121 | 0.41 | 0.75 | 24 | empty |
Compared structures
- 4LJA · ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RA63 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (Q9RA63) · 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 Q9RA63
- Elsewhere: RCSB PDB 4LJA · PDBe 4LJA · UniProt Q9RA63
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