MolNFT v2 · #125457 · protein
Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima
5KYM · 1-acyl-sn-glycerol-3-phosphate acyltransferase: “Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima”. X-ray diffraction at 2.8, 1 ligand (HGX), 5 pockets (best druggability…
- PDB
- 5KYM
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
- Molecule
- 1-acyl-sn-glycerol-3-phosphate acyltransferase
- EC
- 2.3.1.51
- UniProt
- R4NS39
- Ligands
- HGX
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) | protein | 241 | 50% helix, 12% strand | R4NS39 |
| B | 1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) | protein | 232 | 49% helix, 11% strand | R4NS39 |
Ligands and binding sites
- HGX · 1-heptadecanoyl-2-tridecanoyl-3-glycerol-phosphonyl choline · ligand · 6 copies · chains A, B
- DD9 · nonane · additive · 2 copies · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.77 | 0.81 | 56 | DD9 |
| 2 | 641 | 0.74 | 0.80 | 57 | DD9 |
| 3 | 142 | 0.42 | 0.75 | 27 | empty |
| 4 | 144 | 0.41 | 0.73 | 18 | empty |
| 5 | 144 | 0.39 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KYM · Crystal structure of the 1-acyl-sn-glycerophosphate (lpa) acyltransferase, plsc, from… · 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 R4NS39
- Elsewhere: RCSB PDB 5KYM · PDBe 5KYM · UniProt R4NS39
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