Research workbench
Crystal structure of glucuronoyl esterase from cerrena unicolor covalent complex with the aldouronic acid uxxr
Analyse Crystal structure of glucuronoyl esterase from cerrena unicolor covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RV8
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-O-methyl-glucuronoyl methylesterase
- EC
- 3.1.1.-
- UniProt
- A0A0A7EQR3
- Ligands
- XYL, GCV, XYP, MAN, NAG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-O-methyl-glucuronoyl methylesterase (EC 3.1.1.-) | protein | 381 | 35% helix, 19% strand | A0A0A7EQR3 |
Ligands and binding sites
- XYL · Xylitol · ligand · chains B
- GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · chains B
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.58 | 0.75 | 52 | empty |
| 2 | 50 | 0.34 | 0.79 | 12 | empty |
| 3 | 61 | 0.27 | 0.73 | 16 | empty |
| 4 | 55 | 0.25 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 380 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 1 covalent (disulfide, O-glycosylation, N-glycosylation, covalent ligand).
Compared structures
- 6RV8 · Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor covalent complex with the… · 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
- Every structure of UniProt A0A0A7EQR3
- Elsewhere: RCSB PDB 6RV8 · PDBe 6RV8 · UniProt A0A0A7EQR3
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