MolNFT v1 · #89196 · protein
Crystal structure of nucleoside-diphosphate kinase from borrelia burgdorferi
4DI6 · Nucleoside diphosphate kinase: “Crystal structure of nucleoside-diphosphate kinase from borrelia burgdorferi”. X-ray diffraction, 12 pockets (best druggability 0.87). MolNFT v1 #89196 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DI6
- Type
- protein
- Length
- 1,009 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- O51419
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 169 | 47% helix, 19% strand | O51419 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 166 | 48% helix, 19% strand | O51419 |
| E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 168 | 48% helix, 19% strand | O51419 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.87 | 0.89 | 88 | empty |
| 2 | 271 | 0.60 | 0.79 | 34 | empty |
| 3 | 277 | 0.58 | 0.78 | 31 | empty |
| 4 | 317 | 0.58 | 0.77 | 34 | empty |
| 5 | 277 | 0.58 | 0.78 | 34 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1128 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1113 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1096 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4DI6 · crystal structure of nucleoside-diphosphate kinase from Borrelia burgdorferi · the same entry in another collection · chain D against D, TM-score 1.00
- O51419 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (O51419) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O51419
- Elsewhere: RCSB PDB 4DI6 · PDBe 4DI6 · UniProt O51419
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