MolNFT v1 · #118481 · protein
Crystal structure of membrane associated pata from mycobacterium smegmatis in complex with S-hexadecyl coenzyme a - P21 space group
5F34 · Phosphatidylinositol mannoside acyltransferase: “Crystal structure of membrane associated pata from mycobacterium smegmatis in complex with S-hexadecyl…”. X-ray diffraction, 1 ligand (HD6), 10 pockets (best druggability 0.79).…
- PDB
- 5F34
- Type
- protein
- Length
- 1,011 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
- HD6
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 253 | 49% helix, 19% strand | A0QWG5 |
| C | Phosphatidylinositol mannoside acyltransferase (EC 2.3.1.-) | protein | 252 | 48% helix, 19% strand | A0QWG5 |
Ligands and binding sites
- HD6 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S})-4-[[3-(2-hexadecylsulfanylethylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.79 | 0.82 | 77 | HD6 |
| 2 | 699 | 0.78 | 0.82 | 67 | HD6 |
| 3 | 656 | 0.76 | 0.81 | 62 | HD6 |
| 4 | 768 | 0.76 | 0.80 | 72 | HD6 |
| 5 | 305 | 0.55 | 0.75 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 972 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 834 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 197 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5F34 · Crystal structure of membrane associated PatA from Mycobacterium smegmatis in complex… · 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 A 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 5F34 · PDBe 5F34 · UniProt A0QWG5
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