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The crystal structure of an ADP complex of bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution
Analyse The crystal structure of an ADP complex of bacillus subtilis pyridoxal kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I5B
- Type
- protein
- Length
- 1,326 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomethylpyrimidine kinase
- EC
- 2.7.4.7
- UniProt
- P39610
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 269 | 41% helix, 22% strand | P39610 |
| C | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 265 | 40% helix, 22% strand | P39610 |
| D, E | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 267 | 41% helix, 23% strand | P39610 |
| B | Phosphomethylpyrimidine kinase (EC 2.7.4.7) | protein | 258 | 43% helix, 23% strand | P39610 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, C, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.83 | 0.84 | 125 | ADP |
| 2 | 933 | 0.83 | 0.84 | 116 | ADP |
| 3 | 406 | 0.69 | 0.81 | 49 | ADP |
| 4 | 225 | 0.65 | 0.83 | 40 | empty |
| 5 | 78 | 0.39 | 0.78 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1968 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1956 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 709 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 572 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2I5B · The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides… · the same entry in another collection · chain E against E, TM-score 1.00
- P39610 · AlphaFold monomer V2.0 prediction for pyridoxine kinase (P39610) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P39610
- Elsewhere: RCSB PDB 2I5B · PDBe 2I5B · UniProt P39610
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