MolNFT v1 · #93154 · protein
Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with the GM2 glycan
4GU3 · Outer capsid protein sigma-1: “Crystal structure of the T1L reovirus attachment protein SIGMA1 in complex with the GM2 glycan”. X-ray diffraction, 4 ligands (BGC, GAL, SIA), 4 pockets (best druggability 0.85). MolNFT v1 #93154 on…
- 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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