Research workbench
Tailspike protein of SF6 bacteriophage bound to shigella flexneri O- antigen octasaccharide fragment
Analyse Tailspike protein of SF6 bacteriophage bound to shigella flexneri O- antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4URR
- Type
- protein
- Length
- 3,050 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional tail protein
- EC
- 3.2.1.-
- UniProt
- Q9XJP3
- Ligands
- RAM, NAG, MN, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bifunctional tail protein (EC 3.2.1.-) | protein | 509 | 8% helix, 45% strand | Q9XJP3 |
| B, D, E, F | Bifunctional tail protein (EC 3.2.1.-) | protein | 508 | 7% helix, 45% strand | Q9XJP3 |
Ligands and binding sites
- RAM · alpha-L-rhamnopyranose · sugar · 36 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.86 | 0.94 | 49 | MN, EDO |
| 2 | 445 | 0.86 | 0.94 | 50 | MN, EDO |
| 3 | 716 | 0.86 | 0.89 | 101 | PO4 |
| 4 | 725 | 0.85 | 0.89 | 100 | PO4 |
| 5 | 1132 | 0.84 | 0.85 | 121 | empty |
Interfaces
8 interfaces between chains.
- D–F · 3406 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 3400 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3397 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 3388 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 3375 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 4URR · Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen… · 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 Q9XJP3
- Elsewhere: RCSB PDB 4URR · PDBe 4URR · UniProt Q9XJP3
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