Research workbench
Crystal structure of human carboxylesterase in complex with coenzyme a
Analyse Crystal structure of human carboxylesterase in complex with coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H7C
- 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
- P23141
- Ligands
- COA, NAG, SIA, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 532 | 38% helix, 17% strand | P23141 |
| B, C, E, F | Liver carboxylesterase 1 (EC 3.1.1.1) | protein | 531 | 38% helix, 17% strand | P23141 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, F, B, D, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, F, B, C, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains D, F, E
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D, E, F
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 | 1092 | 0.88 | 0.89 | 110 | COA |
| 2 | 1054 | 0.88 | 0.89 | 94 | COA |
| 3 | 1085 | 0.88 | 0.88 | 106 | COA |
| 4 | 827 | 0.79 | 0.82 | 111 | SO4 |
| 5 | 1077 | 0.78 | 0.80 | 123 | SO4 |
Interfaces
9 interfaces between chains.
- C–E · 1998 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1871 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 1871 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 551 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2H7C · Crystal structure of human carboxylesterase in complex with Coenzyme A · 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 2H7C · PDBe 2H7C · UniProt P23141
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