Research workbench
Crystal structure of membrane associated pata from mycobacterium smegmatis in complex with palmitate - P21 space group
Analyse Crystal structure of membrane associated pata from mycobacterium smegmatis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2Z
- Type
- protein
- Length
- 1,003 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
- PLM
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 248 | 49% helix, 19% strand | A0QWG5 |
| B | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 254 | 48% helix, 19% strand | A0QWG5 |
| C | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 245 | 48% helix, 19% strand | A0QWG5 |
| D | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 256 | 48% helix, 19% strand | A0QWG5 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.79 | 0.81 | 80 | PLM |
| 2 | 1120 | 0.78 | 0.79 | 93 | PLM |
| 3 | 914 | 0.78 | 0.80 | 64 | PLM |
| 4 | 746 | 0.77 | 0.81 | 64 | PLM |
| 5 | 338 | 0.56 | 0.75 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 336 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 324 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 171 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5F2Z · Crystal structure of membrane associated PatA from Mycobacterium smegmatis in complex… · the same entry in another collection · chain A against A, 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 5F2Z · PDBe 5F2Z · UniProt A0QWG5
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