MolNFT v1 · #164769 · protein
Crystal structure of bacteroides thetaiotamicron endobt-3987 in complex with MAN9GLCNAC product in P1
6T8K · Endo-beta-N-acetylglucosaminidase F1: “Crystal structure of bacteroides thetaiotamicron endobt-3987 in complex with MAN9GLCNAC product in P1”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 7 pockets (best druggability 0.79). MolNFT…
- PDB
- 6T8K
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- 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
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase F1 | protein | 431 | 25% helix, 31% strand | Q8A0N4 |
| B | Endo-beta-N-acetylglucosaminidase F1 | protein | 429 | 25% helix, 30% strand | Q8A0N4 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.79 | 0.81 | 131 | empty |
| 2 | 547 | 0.77 | 0.84 | 46 | empty |
| 3 | 547 | 0.76 | 0.83 | 42 | empty |
| 4 | 296 | 0.64 | 0.81 | 37 | empty |
| 5 | 205 | 0.60 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 897 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6T8K · Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc… · 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 6T8K · PDBe 6T8K · UniProt Q8A0N4
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