Research workbench
Crystal structure analysis of an ndp kinase from pyrobaculum aerophilum
Analyse Crystal structure analysis of an ndp kinase 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
- 1XQI
- Type
- protein
- Length
- 546 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q8ZWY4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 182 | 54% helix, 13% strand | Q8ZWY4 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.71 | 0.82 | 38 | TRS, PGE |
| 2 | 486 | 0.70 | 0.80 | 40 | TRS, PGE |
| 3 | 446 | 0.70 | 0.81 | 39 | TRS, PGE |
| 4 | 104 | 0.47 | 0.80 | 20 | empty |
| 5 | 85 | 0.47 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 770 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1XQI · Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZWY4 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q8ZWY4) · a predicted model of the same protein · 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 Q8ZWY4
- Elsewhere: RCSB PDB 1XQI · PDBe 1XQI · UniProt Q8ZWY4
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