MolNFT v1 · #141252 · protein
Structure of bifidobacterium dentium beta-glucuronidase complexed with coumarin-3-O-glucuronide
5Z1B · Glycosyl hydrolase family 2, tim barrel domain protein: “Structure of bifidobacterium dentium beta-glucuronidase complexed with coumarin-3-O-glucuronide”. X-ray diffraction, 2 ligands (SE2, BDP), 20 pockets (best druggability 0.91).…
- PDB
- 5Z1B
- Type
- protein
- Length
- 2,493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 2, tim barrel domain protein
- EC
- 3.2.1.31
- UniProt
- E0QAF3
- Ligands
- SE2, BDP
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 2, tim barrel domain protein (EC 3.2.1.31) | protein | 627 | 22% helix, 34% strand | E0QAF3 |
| B | Glycosyl hydrolase family 2, tim barrel domain protein (EC 3.2.1.31) | protein | 620 | 21% helix, 34% strand | E0QAF3 |
| C | Glycosyl hydrolase family 2, tim barrel domain protein (EC 3.2.1.31) | protein | 624 | 21% helix, 34% strand | E0QAF3 |
| D | Glycosyl hydrolase family 2, tim barrel domain protein (EC 3.2.1.31) | protein | 622 | 21% helix, 34% strand | E0QAF3 |
Ligands and binding sites
- SE2 · 3-hydroxy-2H-chromen-2-one · ligand · 4 copies · chains A, B, C, D
- BDP · beta-D-glucopyranuronic acid · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.91 | 0.94 | 142 | empty |
| 2 | 1090 | 0.86 | 0.87 | 110 | empty |
| 3 | 639 | 0.85 | 0.89 | 83 | empty |
| 4 | 205 | 0.82 | 0.96 | 36 | empty |
| 5 | 717 | 0.74 | 0.80 | 81 | BDP, SE2 |
Interfaces
6 interfaces between chains.
- B–D · 2424 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2405 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2263 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2245 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5Z1B · Structure of Bifidobacterium dentium beta-glucuronidase complexed with… · 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 E0QAF3
- Elsewhere: RCSB PDB 5Z1B · PDBe 5Z1B · UniProt E0QAF3
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