Research workbench
Hexagonal crystal form P61 of the aquifex aeolicus nucleoside diphosphate kinase
Analyse Hexagonal crystal form P61 of the aquifex aeolicus nucleoside diphosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZTQ
- Type
- protein
- Length
- 1,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- O67528
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 141 | 48% helix, 20% strand | O67528 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.85 | 0.86 | 70 | empty |
| 2 | 928 | 0.84 | 0.86 | 67 | empty |
| 3 | 347 | 0.56 | 0.75 | 31 | empty |
| 4 | 313 | 0.55 | 0.75 | 34 | empty |
| 5 | 305 | 0.54 | 0.75 | 33 | empty |
Interfaces
13 interfaces between chains.
- C–D · 750 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 748 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 748 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 748 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 537 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ZTQ · Hexagonal crystal form P61 of the Aquifex aeolicus nucleoside diphosphate kinase · the same entry in another collection · chain H against H, TM-score 1.00
- O67528 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (O67528) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O67528
- Elsewhere: RCSB PDB 3ZTQ · PDBe 3ZTQ · UniProt O67528
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