MolNFT v1 · #15727 · protein
The awd nucleotide diphosphate kinase from drosophila
1NDL · Nucleoside diphosphate kinase: “The awd nucleotide diphosphate kinase from drosophila”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #15727 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NDL
- Type
- protein
- Length
- 456 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
- P08879
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 49% helix, 14% strand | P08879 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.63 | 0.79 | 27 | empty |
| 2 | 226 | 0.48 | 0.74 | 29 | empty |
| 3 | 217 | 0.47 | 0.74 | 32 | empty |
| 4 | 151 | 0.43 | 0.75 | 26 | empty |
| 5 | 111 | 0.43 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 890 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 878 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 P08879
- Elsewhere: RCSB PDB 1NDL · PDBe 1NDL · UniProt P08879
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