MolNFT v1 · #135379 · protein
Crystal structure of LECITHIN:CHOLESTEROL acyltransferase (lcat) in a closed conformation
5TXF · Phosphatidylcholine-sterol acyltransferase: “Crystal structure of LECITHIN:CHOLESTEROL acyltransferase (lcat) in a closed conformation”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #135379…
- PDB
- 5TXF
- Type
- protein
- Length
- 1,512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylcholine-sterol acyltransferase
- EC
- 2.3.1.43
- UniProt
- P04180
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) | protein | 378 | 31% helix, 23% strand | P04180 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.79 | 0.98 | 27 | empty |
| 2 | 601 | 0.79 | 0.84 | 91 | empty |
| 3 | 117 | 0.77 | 0.96 | 24 | empty |
| 4 | 114 | 0.76 | 0.96 | 25 | empty |
| 5 | 463 | 0.76 | 0.85 | 76 | empty |
Interfaces
5 interfaces between chains.
- A–C · 647 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 538 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5TXF · Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in a closed conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P04180 · AlphaFold monomer V2.0 prediction for phosphatidylcholine-sterol acyltransferase (P04180) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P04180
- Elsewhere: RCSB PDB 5TXF · PDBe 5TXF · UniProt P04180
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