Research workbench
Crystal structure of SPGH29
Analyse Crystal structure of SPGH29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ORH
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A0A0H2US78
- Ligands
- FUC, NDG, GAL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoside hydrolase | protein | 449 | 28% helix, 26% strand | A0A0H2US78 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.78 | 0.87 | 52 | NDG, GAL, FUC |
| 2 | 397 | 0.78 | 0.87 | 55 | NDG, GAL, FUC |
| 3 | 268 | 0.73 | 0.87 | 44 | EDO |
| 4 | 293 | 0.52 | 0.74 | 31 | empty |
| 5 | 69 | 0.41 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6ORH · Crystal structure of SpGH29 · 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 A0A0H2US78
- Elsewhere: RCSB PDB 6ORH · PDBe 6ORH · UniProt A0A0H2US78
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