Research workbench
Ndp kinase mutant (H122G;N119S;F64W) in complex with abazttp
Analyse Ndp kinase mutant (H122G;N119S;F64W) in complex with abazttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MN7
- Type
- protein
- Length
- 300 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ndp kinase
- EC
- 2.7.4.6
- UniProt
- P22887
- Ligands
- ABT, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ndp kinase (EC 2.7.4.6) | protein | 150 | 41% helix, 17% strand | P22887 |
Ligands and binding sites
- ABT · 3'-azido-3'-deoxy-thymidine-5'-alpha borano triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.59 | 0.78 | 36 | empty |
| 2 | 240 | 0.56 | 0.78 | 31 | empty |
| 3 | 173 | 0.52 | 0.79 | 28 | MG, ABT |
| 4 | 174 | 0.49 | 0.77 | 27 | MG, ABT |
| 5 | 97 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1MN7 · NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP · the same entry in another collection · chain A against A, TM-score 1.00
- P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · 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 P22887
- Elsewhere: RCSB PDB 1MN7 · PDBe 1MN7 · UniProt P22887
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