Research workbench
ZG3615, a family 117 glycoside hydrolase in complex with beta-3,6- anhydro-L-galactose
Analyse ZG3615, a family 117 glycoside hydrolase in complex with beta-3,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U6D
- Type
- protein
- Length
- 767 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical periplasmic protein
- EC
- 3.2.1.-
- UniProt
- F0V1E2
- Ligands
- 3DY, CA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved hypothetical periplasmic protein (EC 3.2.1.-) | protein | 382 | 8% helix, 40% strand | F0V1E2 |
| B | Conserved hypothetical periplasmic protein (EC 3.2.1.-) | protein | 385 | 8% helix, 38% strand | F0V1E2 |
Ligands and binding sites
- 3DY · 3,6-anhydro-beta-L-galactopyranose · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.75 | 0.95 | 34 | EDO |
| 2 | 392 | 0.65 | 0.79 | 58 | PEG, 3DY |
| 3 | 489 | 0.64 | 0.77 | 63 | EDO |
| 4 | 120 | 0.40 | 0.75 | 24 | EDO |
| 5 | 66 | 0.39 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 4428 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 4U6D · Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6-anhydro-L-galactose · 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 F0V1E2
- Elsewhere: RCSB PDB 4U6D · PDBe 4U6D · UniProt F0V1E2
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