Research workbench
Structure of Lentithecium fluviatile carbohydrate esterase from the CE15 family (LfCE15C)
Analyse Structure of Lentithecium fluviatile carbohydrate esterase from the CE15 family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B48
- Type
- protein
- Length
- 1,479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Lentithecium fluviatile
- Molecule
- Carbohydrate esterase family 15 protein
- UniProt
- A0A6G1IIU9
- Ligands
- NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.65 · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carbohydrate esterase family 15 protein | protein | 370 | 34% helix, 21% strand | A0A6G1IIU9 |
| D | Carbohydrate esterase family 15 protein | protein | 369 | 34% helix, 20% strand | A0A6G1IIU9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- FMT · Formic acid · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.71 | 0.75 | 68 | empty |
| 2 | 525 | 0.64 | 0.76 | 51 | empty |
| 3 | 275 | 0.64 | 0.81 | 40 | empty |
| 4 | 222 | 0.58 | 0.80 | 36 | empty |
| 5 | 147 | 0.51 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 384 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 334 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
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 A0A6G1IIU9
- Elsewhere: RCSB PDB 8B48 · PDBe 8B48 · UniProt A0A6G1IIU9
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