Research workbench
Crystal structure of the chaperonin from thermococcus strain ks-1 (two-point mutant complexed with AMP-pnp)
Analyse Crystal structure of the chaperonin from thermococcus strain ks-1 (two-point… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q3Q
- Type
- protein
- Length
- 2,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermosome alpha subunit
- EC
- 3.6.4.9
- UniProt
- O24729
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thermosome alpha subunit (EC 3.6.4.9) | protein | 518 | 52% helix, 19% strand | O24729 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.82 | 0.93 | 45 | MG, ANP |
| 2 | 304 | 0.81 | 0.92 | 49 | MG, ANP |
| 3 | 318 | 0.80 | 0.91 | 48 | MG, ANP |
| 4 | 315 | 0.80 | 0.90 | 48 | MG, ANP |
| 5 | 1023 | 0.78 | 0.80 | 102 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3237 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3197 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 925 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1Q3Q · Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant… · 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 O24729
- Elsewhere: RCSB PDB 1Q3Q · PDBe 1Q3Q · UniProt O24729
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