Research workbench
Structure of apo staphylococcus aureus D-tagatose-6-phosphate kinase
Analyse Structure of apo staphylococcus aureus D-tagatose-6-phosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q5R
- Type
- protein
- Length
- 1,243 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
- Q5HE12
- Pockets
- 10 · best druggability 0.73
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 | 318 | 37% helix, 25% strand | Q5HE12 |
| B | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 312 | 37% helix, 26% strand | Q5HE12 |
| C | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 303 | 38% helix, 27% strand | Q5HE12 |
| D | Tagatose-6-phosphate kinase (EC 2.7.1.144) | protein | 310 | 40% helix, 26% strand | Q5HE12 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.73 | 0.78 | 106 | empty |
| 2 | 711 | 0.69 | 0.77 | 82 | empty |
| 3 | 711 | 0.69 | 0.76 | 82 | empty |
| 4 | 517 | 0.68 | 0.79 | 57 | empty |
| 5 | 123 | 0.51 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1553 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1506 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 442 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2Q5R · Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HE12 · AlphaFold monomer V2.0 prediction for tagatose-6-phosphate kinase (Q5HE12) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q5HE12
- Elsewhere: RCSB PDB 2Q5R · PDBe 2Q5R · UniProt Q5HE12
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