MolNFT v1 · #138031 · protein
Crystal structure of bacteriophage CBA120 tailspike protein 4 enzymatically active domain (TSP4DN, ORF213)
5W6H: “Crystal structure of bacteriophage CBA120 tailspike protein 4 enzymatically active domain (TSP4DN, ORF213)”. X-ray diffraction, 5 ligands (K, NA, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #138031 on GenesisL1: 3D…
- PDB
- 5W6H
- Type
- protein
- Length
- 2,091 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tailspike protein 4
- UniProt
- G3M192
- Ligands
- K, NA, ZN, SO4, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tailspike protein 4 | protein | 697 | 10% helix, 39% strand | G3M192 |
Ligands and binding sites
- K · Potassium ion · metal · chains A, B, C
- NA · Sodium ion · metal · chains A, B, C
- ZN · Zinc ion · metal · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B, C
- CL · Chloride ion · ion · chains C
- ACT · Acetate ion · additive · 26 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.87 | 0.91 | 73 | ACT, SO4 |
| 2 | 481 | 0.85 | 0.92 | 63 | SO4 |
| 3 | 371 | 0.84 | 0.93 | 62 | NA |
| 4 | 1060 | 0.84 | 0.85 | 74 | ACT |
| 5 | 118 | 0.77 | 0.97 | 27 | ZN |
Interfaces
3 interfaces between chains.
- B–C · 4096 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 4087 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4086 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 5W6H · Crystal structure of Bacteriophage CBA120 tailspike protein 4 enzymatically active domain… · the same entry in another collection · chain C against C, 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 G3M192
- Elsewhere: RCSB PDB 5W6H · PDBe 5W6H · UniProt G3M192
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