Research workbench
Crystal structure of bacteroides thetaiotamicron endobt-3987 with MAN5GLCNAC product
Analyse Crystal structure of bacteroides thetaiotamicron endobt-3987 with MAN5GLCNAC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCW
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase F1
- UniProt
- Q8A0N4
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase F1 | protein | 428 | 25% helix, 30% strand | Q8A0N4 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.78 | 0.82 | 66 | empty |
| 2 | 252 | 0.60 | 0.80 | 36 | empty |
Compared structures
- 6TCW · Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 with Man5GlcNAc product · 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 Q8A0N4
- Elsewhere: RCSB PDB 6TCW · PDBe 6TCW · UniProt Q8A0N4
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