Research workbench
Crystal structure of a nudix protein from pyrobaculum aerophilum
Analyse Crystal structure of a nudix protein from pyrobaculum aerophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K2E
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix homolog
- UniProt
- Q8ZTD8
- Ligands
- NI, SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudix homolog | protein | 152 | 29% helix, 38% strand | Q8ZTD8 |
| B | Nudix homolog | protein | 150 | 25% helix, 41% strand | Q8ZTD8 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.62 | 0.83 | 31 | NI, GOL, ACY |
| 2 | 139 | 0.58 | 0.84 | 23 | NI, GOL |
| 3 | 203 | 0.54 | 0.77 | 22 | empty |
| 4 | 105 | 0.49 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1558 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1K2E · crystal structure of a nudix protein from Pyrobaculum aerophilum · 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 Q8ZTD8
- Elsewhere: RCSB PDB 1K2E · PDBe 1K2E · UniProt Q8ZTD8
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