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A 3,6-anhydro-D-galactosidase produced by zobellia galactanivorans. this is an exo-lytic enzyme that hydrolyzes terminal 3,6-anhydro-D- galactose from the non-reducing end of carrageenan oligosaccharides.
Analyse A 3,6-anhydro-D-galactosidase produced by zobellia galactanivorans. this is an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OPQ
- Type
- protein
- Length
- 2,635 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,6-anhydro-D-galactosidase
- UniProt
- G0L004
- Ligands
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3,6-anhydro-D-galactosidase | protein | 659 | 24% helix, 32% strand | G0L004 |
| D | 3,6-anhydro-D-galactosidase | protein | 658 | 24% helix, 31% strand | G0L004 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.82 | 0.84 | 95 | MPD, TRS |
| 2 | 889 | 0.82 | 0.84 | 92 | MPD, TRS |
| 3 | 847 | 0.82 | 0.84 | 91 | MPD, TRS |
| 4 | 842 | 0.81 | 0.84 | 88 | MPD, TRS |
| 5 | 66 | 0.62 | 0.92 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3702 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3698 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5OPQ · A 3,6-anhydro-D-galactosidase produced by Zobellia galactanivorans. This is an exo-lytic… · 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 G0L004
- Elsewhere: RCSB PDB 5OPQ · PDBe 5OPQ · UniProt G0L004
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