Research workbench
Structure of a phosphatidylinositol-phosphate synthase (pips) from mycobacterium kansasii
Analyse Structure of a phosphatidylinositol-phosphate synthase (pips) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WM5
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afctd-phosphatidylinositol-phosphate synthase (pips) fusion
- UniProt
- A0A101DFK9, U5WZP7
- Ligands
- 8K6, TCE, XP4, NA, PO4
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Afctd-phosphatidylinositol-phosphate synthase (pips) fusion | protein | 337 | 58% helix, 13% strand | A0A101DFK9, U5WZP7 |
| C | Afctd-phosphatidylinositol-phosphate synthase (pips) fusion | protein | 335 | 59% helix, 13% strand | A0A101DFK9, U5WZP7 |
Ligands and binding sites
- 8K6 · Octadecane · ligand · 24 copies · chains A, C
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains A
- XP4 · 1,2-dimyristoyl-sn-glycero-3-phosphate · ligand · chains A, C
- NA · Sodium ion · metal · 7 copies · chains A, C
- PO4 · Phosphate ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A, C
- GOL · Glycerol · additive · 6 copies · chains A, C
- FLC · Citrate anion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.50 | 0.77 | 27 | 8K6, OLC |
| 2 | 192 | 0.48 | 0.76 | 28 | PO4 |
| 3 | 145 | 0.47 | 0.76 | 18 | empty |
| 4 | 104 | 0.35 | 0.74 | 17 | empty |
| 5 | 99 | 0.35 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 2316 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WM5 · Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii · 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 A0A101DFK9
- Every structure of UniProt U5WZP7
- Elsewhere: RCSB PDB 6WM5 · PDBe 6WM5 · UniProt A0A101DFK9 · UniProt U5WZP7
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