Research workbench
Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi, cubic form, apo
Analyse Crystal structure of nucleoside diphosphate kinase from encephalitozoon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPD
- Type
- protein
- Length
- 294 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q8SRM7
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 147 | 43% helix, 16% strand | Q8SRM7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.55 | 0.78 | 46 | empty |
| 2 | 212 | 0.54 | 0.78 | 29 | empty |
| 3 | 144 | 0.43 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1130 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3MPD · Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi, cubic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SRM7 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q8SRM7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8SRM7
- Elsewhere: RCSB PDB 3MPD · PDBe 3MPD · UniProt Q8SRM7
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