Research workbench
Crystal structure of AD37 fiber knob in complex with GD1A oligosaccharide
Analyse Crystal structure of AD37 fiber knob in complex with GD1A oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N0I
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber
- UniProt
- Q64823
- Ligands
- GAL, SIA, BGC, NGA, ZN
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber | protein | 184 | 3% helix, 44% strand | Q64823 |
| B | Fiber | protein | 185 | 3% helix, 45% strand | Q64823 |
| C | Fiber | protein | 183 | 5% helix, 44% strand | Q64823 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains C, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B, C
- BGC · beta-D-glucopyranose · sugar · chains C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.71 | 0.82 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1057 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1047 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1032 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3N0I · Crystal Structure of Ad37 fiber knob in complex with GD1a oligosaccharide · 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 Q64823
- Elsewhere: RCSB PDB 3N0I · PDBe 3N0I · UniProt Q64823
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