Research workbench
The molecular mechanism of substrate recognition and catalysis of the membrane acyltransferase pata -- complex of pata with palmitate, mannose, and palmitoyl-6-mannose
Analyse The molecular mechanism of substrate recognition and catalysis of the membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCE
- Type
- protein
- Length
- 1,009 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol mannoside acyltransferase
- EC
- 2.3.1.-
- UniProt
- A0QWG5
- Ligands
- 9R2, PLM, BMA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 255 | 48% helix, 19% strand | A0QWG5 |
| B | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 252 | 47% helix, 19% strand | A0QWG5 |
| C | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 247 | 48% helix, 20% strand | A0QWG5 |
Ligands and binding sites
- 9R2 · [(2~{R},3~{S},4~{S},5~{S},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hexadecanoate · ligand · 3 copies · chains A, B, C, D
- PLM · Palmitic acid · ligand · chains A
- BMA · beta-D-mannopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.82 | 0.83 | 95 | PLM, BMA |
| 2 | 849 | 0.82 | 0.84 | 78 | 9R2 |
| 3 | 1058 | 0.81 | 0.82 | 90 | 9R2 |
| 4 | 762 | 0.77 | 0.81 | 61 | 9R2 |
| 5 | 95 | 0.40 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1167 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 226 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 150 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5OCE · THE MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND CATALYSIS OF THE MEMBRANE… · the same entry in another collection · chain D against D, TM-score 1.00
- A0QWG5 · AlphaFold monomer V2.0 prediction for phosphatidylinositol mannoside acyltransferase… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A0QWG5
- Elsewhere: RCSB PDB 5OCE · PDBe 5OCE · UniProt A0QWG5
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