Research workbench
Crystal structure of gkap from geobacillus kaustophilus HTA426
Analyse Crystal structure of gkap from geobacillus kaustophilus HTA426 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TN3
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.5.-.-
- UniProt
- Q5KZU5
- Ligands
- CO
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase (EC 3.5.-.-) | protein | 323 | 44% helix, 15% strand | Q5KZU5 |
| B | Phosphotriesterase (EC 3.5.-.-) | protein | 324 | 47% helix, 15% strand | Q5KZU5 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.67 | 0.82 | 47 | empty |
| 2 | 258 | 0.66 | 0.82 | 38 | empty |
| 3 | 404 | 0.63 | 0.77 | 50 | empty |
| 4 | 93 | 0.42 | 0.78 | 20 | empty |
| 5 | 91 | 0.39 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3TN3 · Crystal structure of GkaP from Geobacillus kaustophilus HTA426 · 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 Q5KZU5
- Elsewhere: RCSB PDB 3TN3 · PDBe 3TN3 · UniProt Q5KZU5
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