Research workbench
Crystal structure of epiphyas postvittana antennal carboxylesterase 24
Analyse Crystal structure of epiphyas postvittana antennal carboxylesterase 24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MP4
- Type
- protein
- Length
- 4,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxylesterase-24
- EC
- 3.1.1.1
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Carboxylesterase-24 (EC 3.1.1.1) | protein | 534 | 37% helix, 18% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 8 copies
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 | 960 | 0.79 | 0.81 | 102 | empty |
| 2 | 664 | 0.79 | 0.83 | 83 | empty |
| 3 | 984 | 0.79 | 0.80 | 103 | empty |
| 4 | 721 | 0.78 | 0.82 | 86 | empty |
| 5 | 132 | 0.73 | 0.93 | 31 | NAG |
Interfaces
9 interfaces between chains.
- A–B · 904 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 903 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 869 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 860 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 481 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7MP4 · Crystal structure of Epiphyas postvittana antennal carboxylesterase 24 · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 7MP4 · PDBe 7MP4
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