MolNFT v1 · #135556 · protein
Crystal structure of a nucleoside diphosphate kinase from naegleria fowleri
5U2I: “Crystal structure of a nucleoside diphosphate kinase from naegleria fowleri”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.77). MolNFT v1 #135556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U2I
- Type
- protein
- Length
- 911 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- Ligands
- MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Nucleoside diphosphate kinase | protein | 151 | 48% helix, 16% strand | — |
| F | Nucleoside diphosphate kinase | protein | 156 | 48% helix, 15% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 3 copies · chains D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.77 | 0.89 | 43 | empty |
| 2 | 246 | 0.76 | 0.89 | 30 | empty |
| 3 | 284 | 0.75 | 0.88 | 34 | empty |
| 4 | 189 | 0.66 | 0.85 | 33 | FMT |
| 5 | 162 | 0.64 | 0.85 | 26 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1000 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 997 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 987 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 851 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 851 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5U2I · Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri · 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
- Elsewhere: RCSB PDB 5U2I · PDBe 5U2I
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