Research workbench
Crystal structure of phosphatidyl mannosyltransferase PimA
Analyse Crystal structure of phosphatidyl mannosyltransferase PimA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NC9
- Type
- protein
- Length
- 1,435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.192
- Source
- Mycobacterium smegmatis
- Molecule
- GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
- EC
- 2.4.1.57
- UniProt
- A0QWG6
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · resolution 3.192 · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase (EC 2.4.1.57) | protein | 369 | 44% helix, 18% strand | A0QWG6 |
| B | GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase (EC 2.4.1.57) | protein | 361 | 41% helix, 19% strand | A0QWG6 |
| C | GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase (EC 2.4.1.57) | protein | 346 | 38% helix, 20% strand | A0QWG6 |
| D | GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase (EC 2.4.1.57) | protein | 359 | 45% helix, 18% strand | A0QWG6 |
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.76 | 0.79 | 96 | empty |
| 2 | 628 | 0.68 | 0.77 | 83 | empty |
| 3 | 542 | 0.68 | 0.78 | 62 | empty |
| 4 | 418 | 0.67 | 0.79 | 51 | empty |
| 5 | 462 | 0.66 | 0.78 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 962 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 942 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 482 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NC9 · Crystal structure of phosphatidyl mannosyltransferase pima · the same entry in another collection · chain D against D, TM-score 1.00
- A0QWG6 · AlphaFold monomer V2.0 prediction for phosphatidyl-myo-inositol mannosyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.88
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 A0QWG6
- Elsewhere: RCSB PDB 4NC9 · PDBe 4NC9 · UniProt A0QWG6
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