MolNFT v1 · #146949 · protein
Crystal structure of parabacteroides merdae beta-glucuronidase (gus)
6DXU · Glycosyl hydrolase family 2, tim barrel domain protein: “Crystal structure of parabacteroides merdae beta-glucuronidase (gus)”. X-ray diffraction, 2 ligands (BCN, NA), 20 pockets (best druggability 0.76). MolNFT v1 #146949 on…
- PDB
- 6DXU
- Type
- protein
- Length
- 3,183 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 2, tim barrel domain protein
- UniProt
- A7AG62
- Ligands
- BCN, NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Glycosyl hydrolase family 2, tim barrel domain protein | protein | 800 | 16% helix, 37% strand | A7AG62 |
| A | Glycosyl hydrolase family 2, tim barrel domain protein | protein | 774 | 16% helix, 38% strand | A7AG62 |
| B | Glycosyl hydrolase family 2, tim barrel domain protein | protein | 803 | 16% helix, 36% strand | A7AG62 |
| C | Glycosyl hydrolase family 2, tim barrel domain protein | protein | 806 | 16% helix, 36% strand | A7AG62 |
Ligands and binding sites
- BCN · Bicine · ligand · 3 copies · chains D, C
- NA · Sodium ion · metal · 8 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.76 | 0.80 | 82 | empty |
| 2 | 675 | 0.74 | 0.80 | 47 | empty |
| 3 | 650 | 0.72 | 0.79 | 47 | empty |
| 4 | 455 | 0.69 | 0.80 | 43 | empty |
| 5 | 518 | 0.69 | 0.79 | 71 | empty |
Interfaces
4 interfaces between chains.
- D–C · 2121 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2044 Ų buried · 36 hydrogen bonds · protein-protein
- D–A · 723 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6DXU · Crystal Structure of Parabacteroides merdae Beta-Glucuronidase (GUS) · the same entry in another collection · chain D against D, 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 A7AG62
- Elsewhere: RCSB PDB 6DXU · PDBe 6DXU · UniProt A7AG62
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