Research workbench
Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with the GM2 glycan
Analyse Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GU3
- Type
- protein
- Length
- 614 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein sigma-1
- UniProt
- P04506
- Ligands
- BGC, GAL, SIA, NGA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer capsid protein sigma-1 | protein | 205 | 4% helix, 57% strand | P04506 |
| C | Outer capsid protein sigma-1 | protein | 204 | 5% helix, 57% strand | P04506 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 3 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.85 | 0.96 | 32 | empty |
| 2 | 349 | 0.71 | 0.84 | 51 | empty |
| 3 | 232 | 0.60 | 0.80 | 27 | empty |
| 4 | 60 | 0.39 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2092 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2077 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2036 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4GU3 · Crystal structure of the T1L reovirus attachment protein sigma1 in complex with the GM2… · 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 P04506
- Elsewhere: RCSB PDB 4GU3 · PDBe 4GU3 · UniProt P04506
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