MolNFT v1 · #158512 · protein
Crystal structure of a tailspike protein 3 (TSP3, ORF212) from escherichia COLI O157:H7 bacteriophage CBA120
6NW9: “Crystal structure of a tailspike protein 3 (TSP3, ORF212) from escherichia COLI O157:H7 bacteriophage CBA120”. X-ray diffraction, 5 ligands (NA, MG, CL), 20 pockets (best druggability 0.85). MolNFT v1 #158512 on GenesisL1: 3D…
- PDB
- 6NW9
- Type
- protein
- Length
- 1,851 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tailspike protein
- UniProt
- G3M191
- Ligands
- NA, MG, CL, CO3, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tailspike protein | protein | 616 | 11% helix, 43% strand | G3M191 |
| B | Tailspike protein | protein | 616 | 12% helix, 43% strand | G3M191 |
| C | Tailspike protein | protein | 619 | 11% helix, 43% strand | G3M191 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- CO3 · Carbonate ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 39 copies · chains A, B, C
- GOL · Glycerol · additive · 34 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, C, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.85 | 0.86 | 85 | PEG, GOL, EDO |
| 2 | 1170 | 0.84 | 0.85 | 76 | EDO |
| 3 | 99 | 0.75 | 0.97 | 21 | empty |
| 4 | 77 | 0.75 | 0.98 | 15 | empty |
| 5 | 58 | 0.74 | 1.00 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4933 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 4871 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4827 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 6NW9 · Crystal structure of a tailspike protein 3 (TSP3, ORF212) from escherichia COLI O157:H7… · 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 G3M191
- Elsewhere: RCSB PDB 6NW9 · PDBe 6NW9 · UniProt G3M191
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