Research workbench
Crystal structure of the putative histidinol phosphatase hisk from listeria monocytogenes with trinuclear metals determined by pixe revealing sulphate ion in active site. based on pixe analysis and original date from 3DCP
Analyse Crystal structure of the putative histidinol phosphatase hisk from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NLR
- Type
- protein
- Length
- 824 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol-phosphatase
- EC
- 3.1.3.15
- UniProt
- A0A3A6YEN9
- Ligands
- MN, CO, FE, CA, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol-phosphatase (EC 3.1.3.15) | protein | 277 | 47% helix, 17% strand | A0A3A6YEN9 |
| B | Histidinol-phosphatase (EC 3.1.3.15) | protein | 273 | 45% helix, 18% strand | A0A3A6YEN9 |
| C | Histidinol-phosphatase (EC 3.1.3.15) | protein | 274 | 46% helix, 18% strand | A0A3A6YEN9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, C
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains B, C
- CA · Calcium ion · metal · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.70 | 0.79 | 67 | SO4 |
| 2 | 203 | 0.63 | 0.83 | 29 | SO4 |
| 3 | 212 | 0.63 | 0.83 | 30 | FE, SO4 |
| 4 | 272 | 0.56 | 0.77 | 39 | empty |
| 5 | 173 | 0.45 | 0.75 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 6NLR · Crystal structure of the putative histidinol phosphatase hisK from Listeria monocytogenes… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A3A6YEN9
- Elsewhere: RCSB PDB 6NLR · PDBe 6NLR · UniProt A0A3A6YEN9
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