Research workbench
Crystal structure of group III chaperonin in the closed state
Analyse Crystal structure of group III chaperonin in the closed state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X9V
- Type
- protein
- Length
- 1,972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermosome, alpha subunit
- UniProt
- Q3AF10
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thermosome, alpha subunit | protein | 493 | 53% helix, 16% strand | Q3AF10 |
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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.80 | 0.81 | 113 | ANP, MG |
| 2 | 317 | 0.78 | 0.89 | 43 | ANP, MG |
| 3 | 326 | 0.76 | 0.88 | 46 | ANP, MG |
| 4 | 690 | 0.75 | 0.81 | 89 | empty |
| 5 | 312 | 0.74 | 0.86 | 41 | ANP, MG |
Interfaces
4 interfaces between chains.
- C–D · 2110 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2076 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 403 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5X9V · Crystal structure of group III chaperonin in the Closed state · 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 Q3AF10
- Elsewhere: RCSB PDB 5X9V · PDBe 5X9V · UniProt Q3AF10
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