Research workbench
Crystal structure of human liver carboxylesterase 1 (HCE1) in covalent complex with the nerve agent soman (gd)
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
- 2HRQ
- Type
- protein
- Length
- 3,188 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver carboxylesterase 1
- EC
- 3.1.1.1
- UniProt
- Q9UK77
- Ligands
- GD7, GLC, FRU, NAG, SIA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 532 | 37% helix, 16% strand | Q9UK77 |
| B, C, E, F | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 531 | 36% helix, 18% strand | Q9UK77 |
Ligands and binding sites
- GD7 · (1R)-1,2,2-trimethylpropyl (R)-methylphosphinate · ligand · 6 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.82 | 133 | SO4, SIA |
| 2 | 868 | 0.80 | 0.82 | 126 | SO4 |
| 3 | 252 | 0.78 | 0.90 | 36 | GD7 |
| 4 | 245 | 0.77 | 0.90 | 36 | GD7 |
| 5 | 236 | 0.77 | 0.90 | 42 | GD7 |
Interfaces
6 interfaces between chains.
- B–C · 567 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 554 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 553 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 547 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 covalent, 6 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 2HRQ · Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in covalent complex with the… · the same entry in another collection · chain C against C, 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 Q9UK77
- Elsewhere: RCSB PDB 2HRQ · PDBe 2HRQ · UniProt Q9UK77
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