MolNFT v1 · #84733 · protein
Orthorhombic crystal form P21212 of the aquifex aeolicus nucleoside diphosphate kinase
3ZTP: “Orthorhombic crystal form P21212 of the aquifex aeolicus nucleoside diphosphate kinase”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.52). MolNFT v1 #84733 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3ZTP
- Type
- protein
- Length
- 282 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
- O67528
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 141 | 49% helix, 20% strand | O67528 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.52 | 0.77 | 25 | SO4 |
| 2 | 241 | 0.52 | 0.76 | 30 | GOL, SO4 |
| 3 | 160 | 0.46 | 0.76 | 16 | empty |
| 4 | 156 | 0.46 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 525 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ZTP · Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase · the same entry in another collection · chain A against A, 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 3ZTP · PDBe 3ZTP · UniProt O67528
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