Research workbench
Crystal structure of human carboxylesterase in complex with homatropine, coenzyme a, and palmitate
Analyse Crystal structure of human carboxylesterase in complex with homatropine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQZ
- 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
- PLM, HTQ, COA, NAG, SIA, SO4, F
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 532 | 37% helix, 16% strand | P23141 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 3 copies · chains A, B, C
- HTQ · Homotropine · ligand · 3 copies · chains A, B, C
- COA · Coenzyme A · ligand · chains 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 · 7 copies · chains A, C, B
- F · Fluoride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.81 | 0.90 | 48 | PLM |
| 2 | 264 | 0.79 | 0.91 | 36 | PLM |
| 3 | 1093 | 0.78 | 0.80 | 116 | SO4 |
| 4 | 277 | 0.77 | 0.89 | 39 | COA |
| 5 | 143 | 0.75 | 0.93 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 558 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 551 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 547 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2DQZ · Crystal structure of human carboxylesterase in complex with homatropine, coenzyme A, and… · 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 2DQZ · PDBe 2DQZ · UniProt P23141
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