MolNFT v1 · #163187 · protein
Crystal structure of glucuronoyl esterase from cerrena unicolor covalent complex with the aldouronic acid uxxr
6RV8 · 4-O-methyl-glucuronoyl methylesterase: “Crystal structure of glucuronoyl esterase from cerrena unicolor covalent complex with the aldouronic acid uxxr”. X-ray diffraction, 5 ligands (XYL, GCV, XYP), 4 pockets (best druggability…
- 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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