Research workbench
Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and ADP
Analyse Transition state mimic of nucleoside-diphosphate kinase from borrelia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DZ6
- Type
- protein
- Length
- 1,008 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
- Ligands
- ADP, VN4, VO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 168 | 49% helix, 18% strand | O51419 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, D
- VN4 · oxido(dioxo)vanadium · ligand · 3 copies · chains A, C, D
- VO4 · Vanadate ion · ion · 3 copies · chains B, E, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.83 | 0.89 | 66 | EDO |
| 2 | 262 | 0.76 | 0.90 | 25 | empty |
| 3 | 247 | 0.64 | 0.82 | 32 | VO4 |
| 4 | 264 | 0.64 | 0.82 | 30 | VO4 |
| 5 | 219 | 0.63 | 0.82 | 31 | ADP, VN4 |
Interfaces
12 interfaces between chains.
- B–D · 1144 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1131 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1125 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1124 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1119 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4DZ6 · Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with… · the same entry in another collection · chain C against C, TM-score 1.00
- O51419 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (O51419) · a predicted model of the same protein · chain A 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 4DZ6 · PDBe 4DZ6 · UniProt O51419
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