MolNFT v1 · #157862 · protein
Crystal structure of hybrid beta-GLUCURONIDASE/BETA-galacturonidase from fusicatenibacter saccharivorans bound to phenyl-thio-beta-D- glucuronide
6NCZ: “Crystal structure of hybrid beta-GLUCURONIDASE/BETA-galacturonidase from fusicatenibacter saccharivorans…”. X-ray diffraction, 1 ligand (FYJ), 20 pockets (best druggability 0.77). MolNFT v1 #157862 on GenesisL1: 3D structure…
- PDB
- 6NCZ
- Type
- protein
- Length
- 3,532 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- A0A174EHD1
- Ligands
- FYJ
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucuronidase (EC 3.2.1.31) | protein | 588 | 23% helix, 32% strand | A0A174EHD1 |
| C, D, E, F | Beta-glucuronidase (EC 3.2.1.31) | protein | 589 | 23% helix, 32% strand | A0A174EHD1 |
Ligands and binding sites
- FYJ · phenyl 1-thio-beta-D-glucopyranosiduronic acid · ligand · 6 copies · chains A, B, C, E, D, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, E, D, 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 | 699 | 0.77 | 0.82 | 62 | empty |
| 2 | 674 | 0.77 | 0.82 | 62 | empty |
| 3 | 664 | 0.77 | 0.82 | 60 | empty |
| 4 | 796 | 0.76 | 0.80 | 85 | empty |
| 5 | 496 | 0.75 | 0.84 | 44 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2859 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2835 Ų buried · 40 hydrogen bonds · protein-protein
- C–E · 2828 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 543 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 539 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6NCZ · Crystal structure of hybrid beta-glucuronidase/beta-galacturonidase from Fusicatenibacter… · 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 A0A174EHD1
- Elsewhere: RCSB PDB 6NCZ · PDBe 6NCZ · UniProt A0A174EHD1
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