MolNFT v1 · #114623 · protein
Crystal structure of human lcat (L4F, N5D) in complex with Fab of an agonistic antibody
5BV7 · Phosphatidylcholine-sterol acyltransferase: “Crystal structure of human lcat (L4F, N5D) in complex with Fab of an agonistic antibody”. X-ray diffraction, 2 ligands (MAN, NAG), 14 pockets (best druggability 0.72). MolNFT v1 #114623…
- PDB
- 5BV7
- Type
- protein
- Length
- 1,241 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylcholine-sterol acyltransferase; 27C3 light chain; 27C3 heavy chain; FAB1…
- EC
- 2.3.1.43
- UniProt
- P04180
- Ligands
- MAN, NAG
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) | protein | 377 | 31% helix, 23% strand | P04180 |
| L | 27C3 light chain | protein | 210 | 9% helix, 51% strand | — |
| H | 27C3 heavy chain | protein | 222 | 7% helix, 54% strand | — |
| B | FAB1 light chain | protein | 212 | 5% helix, 52% strand | — |
| C | FAB1 heavy chain | protein | 220 | 7% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.72 | 0.93 | 28 | empty |
| 2 | 475 | 0.71 | 0.81 | 39 | empty |
| 3 | 140 | 0.64 | 0.87 | 27 | empty |
| 4 | 400 | 0.55 | 0.74 | 56 | empty |
| 5 | 268 | 0.51 | 0.75 | 48 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1820 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1706 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 756 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 695 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 250 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5BV7 · Crystal structure of human LCAT (L4F, N5D) in complex with Fab of an agonistic antibody · 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 0.97
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 5BV7 · PDBe 5BV7 · UniProt P04180
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