Research workbench
Crystal structure of PDGH110B in complex with D-galactose
Analyse Crystal structure of PDGH110B in complex with D-galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JW4
- Type
- protein
- Length
- 1,182 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 110
- Ligands
- GLA, GAL, NI, CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 110 | protein | 591 | 8% helix, 46% strand | — |
| B | Glycoside hydrolase family 110 | protein | 591 | 8% helix, 46% strand | — |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.61 | 0.80 | 48 | GLA |
| 2 | 242 | 0.58 | 0.80 | 42 | GLA |
| 3 | 185 | 0.41 | 0.73 | 30 | empty |
| 4 | 148 | 0.39 | 0.73 | 23 | empty |
| 5 | 95 | 0.34 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 528 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7JW4 · Crystal structure of PdGH110B in complex with D-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
- Elsewhere: RCSB PDB 7JW4 · PDBe 7JW4
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