Research workbench
Crystal structure of the chaperonin from thermococcus strain ks-1 (formiii crystal complexed with ADP)
Analyse Crystal structure of the chaperonin from thermococcus strain ks-1 (formiii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q3S
- Type
- protein
- Length
- 4,136 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermosome alpha subunit
- EC
- 3.6.4.9
- UniProt
- O24729
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Thermosome alpha subunit (EC 3.6.4.9) | protein | 517 | 53% helix, 20% strand | O24729 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, G, H
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 | 875 | 0.82 | 0.84 | 97 | MG, ADP |
| 2 | 272 | 0.81 | 0.92 | 45 | MG, ADP |
| 3 | 266 | 0.80 | 0.92 | 43 | MG, ADP |
| 4 | 261 | 0.80 | 0.92 | 43 | MG, ADP |
| 5 | 277 | 0.80 | 0.91 | 45 | ADP |
Interfaces
16 interfaces between chains.
- B–C · 2545 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2538 Ų buried · 46 hydrogen bonds · protein-protein
- A–H · 2535 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2535 Ų buried · 45 hydrogen bonds · protein-protein
- F–G · 2528 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 1Q3S · Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal… · 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 1Q3S · PDBe 1Q3S · UniProt O24729
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.