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Crystal structure of an N-terminally truncated selenophosphate synthetase from aquifex aeolicus
Analyse Crystal structure of an N-terminally truncated selenophosphate synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZAU
- Type
- protein
- Length
- 914 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenide, water dikinase
- EC
- 2.7.9.3
- UniProt
- O67139
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenide, water dikinase (EC 2.7.9.3) | protein | 307 | 40% helix, 25% strand | O67139 |
| B | Selenide, water dikinase (EC 2.7.9.3) | protein | 303 | 41% helix, 25% strand | O67139 |
| C | Selenide, water dikinase (EC 2.7.9.3) | protein | 304 | 39% helix, 25% strand | O67139 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.52 | 0.76 | 27 | empty |
| 2 | 223 | 0.48 | 0.75 | 29 | empty |
| 3 | 192 | 0.47 | 0.75 | 24 | PO4 |
| 4 | 192 | 0.47 | 0.75 | 24 | empty |
| 5 | 185 | 0.45 | 0.74 | 26 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2ZAU · Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex… · 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 O67139
- Elsewhere: RCSB PDB 2ZAU · PDBe 2ZAU · UniProt O67139
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