Research workbench
Crystal structure of human liver carboxylesterase 1 (HCE1) in covalent complex with the nerve agent cyclosarin (gf)
Analyse Crystal structure of human liver carboxylesterase 1 (HCE1) in covalent complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K9B
- Type
- protein
- Length
- 1,437 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
- WW2
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 485 | 39% helix, 17% strand | P23141 |
| B | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 499 | 38% helix, 17% strand | P23141 |
| C | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 453 | 38% helix, 19% strand | P23141 |
Ligands and binding sites
- WW2 · cyclohexyl (S)-methylphosphonofluoridoate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.78 | 0.80 | 127 | empty |
| 2 | 432 | 0.76 | 0.85 | 45 | WW2 |
| 3 | 552 | 0.73 | 0.81 | 54 | WW2 |
| 4 | 307 | 0.67 | 0.82 | 40 | WW2 |
| 5 | 393 | 0.65 | 0.79 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 572 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 3K9B · Crystal structure of human liver carboxylesterase 1 (hCE1) in covalent complex with the… · 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 C 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 3K9B · PDBe 3K9B · UniProt P23141
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