Research workbench
Crystal structure of human liver carboxylesterase in complex with cleavage products of mevastatin
Analyse Crystal structure of human liver carboxylesterase in complex with cleavage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YA8
- Type
- protein
- Length
- 1,596 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CES1 protein
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- SMB, MVB, NAG, SIA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | CES1 protein (EC 3.1.1.1) | protein | 532 | 37% helix, 17% strand | P23141 |
Ligands and binding sites
- SMB · 2-methylbutanoic acid · ligand · 4 copies · chains A, B, C
- MVB · (1s,7s,8s,8ar)-1,2,3,7,8,8A-hexahydro-7-methyl-8-[2-[(2R,4R)-tetrahydro-4-hy droxy-6-oxo-2H-pyran-2-yl]ethyl]-1-naphthalenol · ligand · 2 copies · chains A, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.81 | 0.89 | 51 | SMB |
| 2 | 381 | 0.81 | 0.89 | 41 | SMB |
| 3 | 998 | 0.80 | 0.82 | 128 | SIA, SO4 |
| 4 | 301 | 0.80 | 0.91 | 44 | SMB |
| 5 | 121 | 0.73 | 0.93 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 567 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 560 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1YA8 · Crystal Structure of Human Liver Carboxylesterase in complex with cleavage products of… · 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 1YA8 · PDBe 1YA8 · UniProt P23141
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