MolNFT v1 · #107835 · protein
Crystallographic structure of nucleoside diphosphate kinase from litopenaeus vannamei complexed with dcdp
4UOG: “Crystallographic structure of nucleoside diphosphate kinase from litopenaeus vannamei complexed with dcdp”. X-ray diffraction, 2 ligands (YYY, MG), 5 pockets (best druggability 0.67). MolNFT v1 #107835 on GenesisL1: 3D structure…
- PDB
- 4UOG
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- A5J299
- Ligands
- YYY, MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 45% helix, 16% strand | A5J299 |
Ligands and binding sites
- YYY · Deoxycytidine diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.67 | 0.79 | 37 | empty |
| 2 | 196 | 0.54 | 0.78 | 29 | YYY, MG |
| 3 | 224 | 0.53 | 0.77 | 29 | YYY, MG |
| 4 | 192 | 0.51 | 0.77 | 27 | YYY, MG |
| 5 | 153 | 0.44 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 753 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 735 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4UOG · Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei… · the same entry in another collection · chain A against A, TM-score 1.00
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 A5J299
- Elsewhere: RCSB PDB 4UOG · PDBe 4UOG · UniProt A5J299
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