Research workbench
Crystal structure of human lcat (L4F, N5D) in complex with Fab of an agonistic antibody
Analyse Crystal structure of human lcat (L4F, N5D) in complex with Fab of an agonistic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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