MolNFT v1 · #110448 · protein
Low resolution structure of lcat in complex with FAB1
4XX1 · FAB1 light chain: “Low resolution structure of lcat in complex with FAB1”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #110448 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XX1
- Type
- protein
- Length
- 2,186 residues
- Chains
- 9
- 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
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, G | FAB1 light chain | protein | 210 | 4% helix, 44% strand | — |
| H | FAB1 heavy chain | protein | 219 | 4% helix, 47% strand | — |
| A, B | Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) | protein | 369 | 30% helix, 23% strand | P04180 |
| E | FAB1 heavy chain | protein | 219 | 8% helix, 50% strand | — |
| O | FAB1 light chain | protein | 105 | 3% helix, 30% strand | — |
| M | FAB1 heavy chain | protein | 124 | 0% helix, 29% strand | — |
| J | Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) | protein | 361 | 29% helix, 22% strand | P04180 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, L, B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.80 | 0.91 | 33 | empty |
| 2 | 399 | 0.77 | 0.86 | 43 | empty |
| 3 | 457 | 0.76 | 0.84 | 50 | empty |
| 4 | 1127 | 0.72 | 0.76 | 93 | empty |
| 5 | 497 | 0.69 | 0.80 | 51 | empty |
Interfaces
15 interfaces between chains.
- G–E · 1767 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1668 Ų buried · 8 hydrogen bonds · protein-protein
- O–M · 794 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 681 Ų buried · 9 hydrogen bonds · protein-protein
- E–B · 660 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4XX1 · Low resolution structure of LCAT in complex with Fab1 · the same entry in another collection · chain J against J, TM-score 1.00
- P04180 · AlphaFold monomer V2.0 prediction for phosphatidylcholine-sterol acyltransferase (P04180) · a predicted model of the same protein · chain J against A, TM-score 0.98
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 4XX1 · PDBe 4XX1 · UniProt P04180
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