Research workbench
Phage 1358 receptor binding protein in complex with the trisaccharide glcnac-galf-glcome
Analyse Phage 1358 receptor binding protein in complex with the trisaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RGA
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage 1358 receptor binding protein (ORF20)
- UniProt
- D3W0F1
- Ligands
- GYP, GZL, NAG
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phage 1358 receptor binding protein (ORF20) | protein | 390 | 8% helix, 41% strand | D3W0F1 |
Ligands and binding sites
- GYP · methyl alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
- GZL · beta-D-galactofuranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.55 | 0.73 | 50 | GYP, NAG |
| 2 | 252 | 0.53 | 0.76 | 29 | empty |
| 3 | 212 | 0.50 | 0.76 | 30 | empty |
| 4 | 163 | 0.40 | 0.73 | 23 | empty |
| 5 | 78 | 0.29 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 217 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RGA · Phage 1358 receptor binding protein in complex with the trisaccharide GlcNAc-Galf-GlcOMe · 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 D3W0F1
- Elsewhere: RCSB PDB 4RGA · PDBe 4RGA · UniProt D3W0F1
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