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Crystal structure of human carboxylesterase in complex with cholate and palmitate
Analyse Crystal structure of human carboxylesterase in complex with cholate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQY
- Type
- protein
- Length
- 1,596 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver carboxylesterase 1
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- CHD, PLM, NAG, SIA, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 532 | 36% helix, 16% strand | P23141 |
Ligands and binding sites
- CHD · Cholic acid · ligand · 3 copies · chains A, B, C
- PLM · Palmitic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
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 | 333 | 0.83 | 0.92 | 38 | PLM |
| 2 | 259 | 0.80 | 0.92 | 50 | PLM |
| 3 | 1094 | 0.78 | 0.80 | 130 | SO4 |
| 4 | 294 | 0.77 | 0.88 | 46 | PLM |
| 5 | 115 | 0.73 | 0.94 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 539 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2DQY · Crystal structure of human carboxylesterase in complex with cholate and palmitate · the same entry in another collection · chain A against A, TM-score 1.00
- P23141 · AlphaFold monomer V2.0 prediction for liver carboxylesterase 1 (P23141) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P23141
- Elsewhere: RCSB PDB 2DQY · PDBe 2DQY · UniProt P23141
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