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Structure of staphylococcus aureus D-tagatose-6-phosphate kinase with cofactor and substrate
Analyse Structure of staphylococcus aureus D-tagatose-6-phosphate kinase with cofactor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JG1
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tagatose-6-phosphate kinase
- EC
- 2.7.1.144
- UniProt
- P0A0B9
- Ligands
- ANP, TA6, MG
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 318 | 38% helix, 26% strand | P0A0B9 |
| C | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 315 | 39% helix, 26% strand | P0A0B9 |
| D | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 313 | 37% helix, 26% strand | P0A0B9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- TA6 · 6-O-phosphono-beta-D-tagatofuranose · ligand · chains B, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.73 | 0.81 | 76 | MG, TA6, ANP |
| 2 | 700 | 0.69 | 0.77 | 80 | MG, ANP |
| 3 | 720 | 0.68 | 0.76 | 80 | MG, ANP |
| 4 | 663 | 0.67 | 0.76 | 77 | MG, ANP |
| 5 | 486 | 0.65 | 0.77 | 54 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1632 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1461 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 356 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 231 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 91 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2JG1 · STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE with cofactor and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0B9 · AlphaFold monomer V2.0 prediction for tagatose-6-phosphate kinase (P0A0B9) · a predicted model of the same protein · chain D 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 P0A0B9
- Elsewhere: RCSB PDB 2JG1 · PDBe 2JG1 · UniProt P0A0B9
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