MolNFT v1 · #139244 · protein
Crystal structure of group III chaperonin in the open state
5X9U · Thermosome, alpha subunit: “Crystal structure of group III chaperonin in the open state”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.83). MolNFT v1 #139244 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5X9U
- Type
- protein
- Length
- 1,976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermosome, alpha subunit
- UniProt
- Q3AF10
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thermosome, alpha subunit | protein | 494 | 52% helix, 14% strand | Q3AF10 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.83 | 0.96 | 30 | empty |
| 2 | 784 | 0.79 | 0.83 | 75 | empty |
| 3 | 662 | 0.73 | 0.80 | 68 | ADP |
| 4 | 55 | 0.72 | 0.98 | 18 | empty |
| 5 | 569 | 0.72 | 0.80 | 56 | ADP |
Interfaces
5 interfaces between chains.
- B–C · 1048 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1044 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 814 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 759 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X9U · Crystal structure of group III chaperonin in the open state · the same entry in another collection · chain B against B, 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 5X9U · PDBe 5X9U · UniProt Q3AF10
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