Research workbench
Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in complex with manganese and citrate
Analyse Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H5A
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.88
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- CDP-diacylglycerol--inositol 3-phosphatidyltransferase
- EC
- 2.7.8.11
- UniProt
- P9WPG7
- Ligands
- LFA, MN, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.88 · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) | protein | 207 | 74% helix, 1% strand | P9WPG7 |
| B | CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) | protein | 209 | 71% helix, 2% strand | P9WPG7 |
Ligands and binding sites
- LFA · Eicosane · ligand · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 7 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- FLC · Citrate anion · additive · 3 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.71 | 0.81 | 49 | MN, FLC |
| 2 | 264 | 0.55 | 0.76 | 25 | OLC, LFA |
| 3 | 245 | 0.54 | 0.76 | 26 | LFA |
| 4 | 150 | 0.46 | 0.77 | 30 | MN, FLC |
| 5 | 73 | 0.35 | 0.76 | 13 | OLC |
Interfaces
1 interface between chains.
- A–B · 2739 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6H5A · Crystal structure of mycobacterium tuberculosis phosphatidylinositol phosphate synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPG7 · AlphaFold monomer V2.0 prediction for phosphatidylinositol phosphate synthase (P9WPG7) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P9WPG7
- Elsewhere: RCSB PDB 6H5A · PDBe 6H5A · UniProt P9WPG7
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