MolNFT v1 · #23846 · protein
X-ray structure of human nucleoside diphosphate kinase a complexed with ADP at 2 a resolution
1UCN: “X-ray structure of human nucleoside diphosphate kinase a complexed with ADP at 2 a resolution”. X-ray diffraction, 3 ligands (ADP, CA, PO4), 8 pockets (best druggability 0.71). MolNFT v1 #23846 on GenesisL1: 3D structure, binding…
- PDB
- 1UCN
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase a
- EC
- 2.7.4.6
- UniProt
- P15531
- Ligands
- ADP, CA, PO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 151 | 48% helix, 16% strand | P15531 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 5 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.71 | 0.83 | 46 | empty |
| 2 | 290 | 0.61 | 0.79 | 33 | PO4, CA, ADP |
| 3 | 240 | 0.60 | 0.80 | 31 | PO4, CA, ADP |
| 4 | 222 | 0.58 | 0.80 | 33 | PO4, CA, ADP |
| 5 | 141 | 0.41 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 840 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 831 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 823 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1UCN · X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P15531 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase a (P15531) · 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 P15531
- Elsewhere: RCSB PDB 1UCN · PDBe 1UCN · UniProt P15531
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