MolNFT v1 · #110429 · protein
Crystal structure of lcat (C31Y) in complex with FAB1
4XWG · FAB1 light chain: “Crystal structure of lcat (C31Y) in complex with FAB1”. X-ray diffraction, 2 ligands (NAG, ZN), 7 pockets (best druggability 0.80). MolNFT v1 #110429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XWG
- Type
- protein
- Length
- 800 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB1 light chain; FAB1 heavy chain; Phosphatidylcholine-sterol acyltransferase
- EC
- 2.3.1.43
- UniProt
- P04180
- Ligands
- NAG, ZN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | FAB1 light chain | protein | 210 | 4% helix, 52% strand | — |
| H | FAB1 heavy chain | protein | 221 | 10% helix, 51% strand | — |
| A | Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) | protein | 369 | 32% helix, 22% strand | P04180 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- ZN · Zinc ion · metal · 16 copies · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.80 | 0.89 | 39 | ZN |
| 2 | 250 | 0.63 | 0.81 | 31 | empty |
| 3 | 128 | 0.61 | 0.86 | 27 | empty |
| 4 | 262 | 0.52 | 0.75 | 35 | empty |
| 5 | 175 | 0.44 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1735 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 660 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 325 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4XWG · Crystal Structure of LCAT (C31Y) in complex with Fab1 · the same entry in another collection · chain L against L, 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 4XWG · PDBe 4XWG · UniProt P04180
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