Research workbench
Ndp kinase in complex with adenosine phosphonoacetic acid
Analyse Ndp kinase in complex with adenosine phosphonoacetic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5Z
- Type
- protein
- Length
- 900 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase, cytosolic
- EC
- 2.7.4.6
- UniProt
- P22887
- Ligands
- SON, PO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6) | protein | 150 | 43% helix, 17% strand | P22887 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.81 | 0.86 | 70 | empty |
| 2 | 785 | 0.80 | 0.83 | 73 | empty |
| 3 | 591 | 0.79 | 0.85 | 63 | empty |
| 4 | 426 | 0.78 | 0.87 | 59 | empty |
| 5 | 198 | 0.57 | 0.80 | 30 | SON |
Interfaces
9 interfaces between chains.
- C–D · 778 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 772 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 767 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 760 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 760 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1S5Z · NDP kinase in complex with adenosine phosphonoacetic acid · the same entry in another collection · chain C against C, 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 1S5Z · PDBe 1S5Z · UniProt P22887
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