MolNFT v1 · #41217 · protein
Structure of staphylococcus aureus D-tagatose-6-phosphate kinase in complex with ADP
2JGV: “Structure of staphylococcus aureus D-tagatose-6-phosphate kinase in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 12 pockets (best druggability 0.72). MolNFT v1 #41217 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2JGV
- Type
- protein
- Length
- 1,249 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
- ADP
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 314 | 39% helix, 26% strand | P0A0B9 |
| B | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 314 | 39% helix, 26% strand | P0A0B9 |
| C | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 311 | 38% helix, 27% strand | P0A0B9 |
| D | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 310 | 39% helix, 25% strand | P0A0B9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, 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 | 660 | 0.72 | 0.79 | 67 | ADP |
| 2 | 599 | 0.71 | 0.79 | 75 | empty |
| 3 | 692 | 0.68 | 0.77 | 79 | empty |
| 4 | 617 | 0.66 | 0.76 | 73 | ADP |
| 5 | 333 | 0.66 | 0.81 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1512 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1485 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2JGV · STRUCTURE OF Staphylococcus aureus D-TAGATOSE-6-PHOSPHATE KINASE in complex with ADP · the same entry in another collection · chain D against D, TM-score 1.00
- P0A0B9 · AlphaFold monomer V2.0 prediction for tagatose-6-phosphate kinase (P0A0B9) · 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 P0A0B9
- Elsewhere: RCSB PDB 2JGV · PDBe 2JGV · UniProt P0A0B9
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