Research workbench
The crystal structure of the protein cina with unknown function from thermoplasma acidophilum
Analyse The crystal structure of the protein cina with unknown function from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KBQ
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein TA0487
- UniProt
- Q9HKV6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein TA0487 | protein | 164 | 43% helix, 24% strand | Q9HKV6 |
| B | Protein TA0487 | protein | 169 | 41% helix, 24% strand | Q9HKV6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.74 | 0.97 | 33 | empty |
| 2 | 50 | 0.50 | 0.87 | 17 | empty |
| 3 | 52 | 0.50 | 0.86 | 19 | empty |
| 4 | 70 | 0.32 | 0.75 | 21 | SO4 |
| 5 | 60 | 0.28 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1002 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3KBQ · The crystal structure of the protein CinA with unknown function from Thermoplasma… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HKV6 · AlphaFold monomer V2.0 prediction for protein TA0487 (Q9HKV6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HKV6
- Elsewhere: RCSB PDB 3KBQ · PDBe 3KBQ · UniProt Q9HKV6
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