MolNFT v1 · #15191 · protein
Crystal structure of human liver carboxylesterase in complex with tacrine
1MX1: “Crystal structure of human liver carboxylesterase in complex with tacrine”. X-ray diffraction, 4 ligands (THA, NAG, SIA), 20 pockets (best druggability 0.89). MolNFT v1 #15191 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1MX1
- Type
- protein
- Length
- 3,187 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver carboxylesterase I
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- THA, NAG, SIA, NDG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Liver carboxylesterase I (EC 3.1.1.1) | protein | 532 | 37% helix, 17% strand | P23141 |
| B, C, D, E, F | Liver carboxylesterase I (EC 3.1.1.1) | protein | 531 | 38% helix, 17% strand | P23141 |
Ligands and binding sites
- THA · Tacrine · ligand · 6 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, A, B, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B, C, D, E, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.89 | 0.90 | 113 | THA |
| 2 | 1084 | 0.89 | 0.90 | 118 | THA |
| 3 | 1173 | 0.88 | 0.89 | 141 | THA |
| 4 | 1038 | 0.81 | 0.82 | 146 | empty |
| 5 | 862 | 0.79 | 0.82 | 116 | empty |
Interfaces
9 interfaces between chains.
- A–F · 2009 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1991 Ų buried · 30 hydrogen bonds · protein-protein
- B–E · 1954 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 564 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 7 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 1MX1 · Crystal Structure of Human Liver Carboxylesterase in complex with tacrine · the same entry in another collection · chain F against F, TM-score 1.00
- P23141 · AlphaFold monomer V2.0 prediction for liver carboxylesterase 1 (P23141) · a predicted model of the same protein · chain E 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 1MX1 · PDBe 1MX1 · UniProt P23141
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