Research workbench
Crystal structure analysis of a recombinant predicted acetamidase/ formamidase from the thermophile thermoanaerobacter tengcongensis
Analyse Crystal structure analysis of a recombinant predicted acetamidase/ formamidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TKK
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted ACETAMIDASE/FORMAMIDASE
- UniProt
- Q8R8S5
- Ligands
- CA, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Predicted ACETAMIDASE/FORMAMIDASE | protein | 301 | 13% helix, 40% strand | Q8R8S5 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- ZN · Zinc 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.73 | 0.79 | 80 | empty |
| 2 | 293 | 0.55 | 0.76 | 52 | empty |
| 3 | 304 | 0.55 | 0.75 | 47 | empty |
| 4 | 147 | 0.51 | 0.79 | 23 | empty |
| 5 | 142 | 0.51 | 0.80 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2385 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2373 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 351 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 254 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 232 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3TKK · Crystal Structure Analysis of a recombinant predicted acetamidase/ formamidase from the… · 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 Q8R8S5
- Elsewhere: RCSB PDB 3TKK · PDBe 3TKK · UniProt Q8R8S5 · AlphaFold DB Q8R8S5
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