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
- 6ORF
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPGH29
- UniProt
- A0A0H2US78
- Ligands
- NDG, FUC, GAL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SPGH29 | protein | 449 | 28% helix, 26% strand | A0A0H2US78 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.84 | 0.85 | 119 | NDG, FUC, GAL, EDO |
| 2 | 533 | 0.78 | 0.84 | 50 | NDG, FUC, GAL |
| 3 | 341 | 0.55 | 0.74 | 32 | empty |
| 4 | 78 | 0.43 | 0.80 | 19 | empty |
| 5 | 71 | 0.42 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1138 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6ORF · 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 6ORF · PDBe 6ORF · UniProt A0A0H2US78
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