Research workbench
Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) in apo form
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
- 6H53
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Mycobacterium tuberculosis H37Rv
- Molecule
- CDP-diacylglycerol--inositol 3-phosphatidyltransferase
- EC
- 2.7.8.11
- UniProt
- P9WPG6
- Ligands
- UPL, SO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) | protein | 190 | 77% helix, 1% strand | P9WPG6 |
| B | CDP-diacylglycerol--inositol 3-phosphatidyltransferase (EC 2.7.8.11) | protein | 191 | 78% helix, 1% strand | P9WPG6 |
Ligands and binding sites
- UPL · Unknown branched fragment of phospholipid · ligand · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.55 | 0.77 | 27 | UPL |
| 2 | 246 | 0.54 | 0.76 | 28 | UPL |
| 3 | 241 | 0.51 | 0.76 | 37 | SO4 |
| 4 | 170 | 0.45 | 0.75 | 29 | SO4 |
| 5 | 66 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2270 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6H53 · Crystal structure of mycobacterium tuberculosis phosphatidylinositol phosphate synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPG6 · AlphaFold monomer V2.0 prediction for phosphatidylinositol phosphate synthase (P9WPG6) · a predicted model of the same protein · chain B 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 P9WPG6
- Elsewhere: RCSB PDB 6H53 · PDBe 6H53 · UniProt P9WPG6
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