Research workbench
Crystal structure of human liver carboxylesterase in complexed with naloxone methiodide, a heroin analogue
Analyse Crystal structure of human liver carboxylesterase in complexed with naloxone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MX9
- Type
- protein
- Length
- 6,378 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver carboxylesterase I
- EC
- 3.1.1.1
- UniProt
- P23141
- Ligands
- NLX, NAG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, J | Liver carboxylesterase I (EC 3.1.1.1) | protein | 532 | 36% helix, 16% strand | P23141 |
| C, E, F, H, I, K, L | Liver carboxylesterase I (EC 3.1.1.1) | protein | 531 | 37% helix, 16% strand | P23141 |
| D | Liver carboxylesterase I (EC 3.1.1.1) | protein | 533 | 35% helix, 17% strand | P23141 |
Ligands and binding sites
- NLX · (5A,17R)-4,5-epoxy-3,14-dihydroxy-17-methyl-6-oxo-17-(2-propenyl)-morphinanium · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K
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 | 1074 | 0.89 | 0.90 | 115 | NLX |
| 2 | 1107 | 0.89 | 0.90 | 106 | NLX |
| 3 | 1145 | 0.89 | 0.90 | 112 | NLX |
| 4 | 1095 | 0.89 | 0.90 | 105 | NLX |
| 5 | 1139 | 0.88 | 0.89 | 116 | NLX |
Interfaces
19 interfaces between chains.
- H–K · 2035 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2028 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 2017 Ų buried · 28 hydrogen bonds · protein-protein
- G–L · 1994 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 1963 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
Compared structures
- 1MX9 · Crystal Structure of Human Liver Carboxylesterase in complexed with naloxone methiodide… · the same entry in another collection · chain L against L, 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 1MX9 · PDBe 1MX9 · UniProt P23141
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