MolNFT v1 · #106266 · protein
Crystal structure of the tailspike protein GP49 from pseudomonas phage LKA1
4RU4 · Tail spike protein GP49: “Crystal structure of the tailspike protein GP49 from pseudomonas phage LKA1”. X-ray diffraction, 2 ligands (NA, CA), 20 pockets (best druggability 0.86). MolNFT v1 #106266 on GenesisL1: 3D structure…
- PDB
- 4RU4
- Type
- protein
- Length
- 3,538 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail spike protein GP49
- UniProt
- Q0E5W5
- Ligands
- NA, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tail spike protein GP49 | protein | 589 | 6% helix, 50% strand | Q0E5W5 |
| B, D, E, F | Tail spike protein GP49 | protein | 590 | 6% helix, 49% strand | Q0E5W5 |
Ligands and binding sites
- NA · Sodium ion · metal · 21 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.86 | 0.96 | 39 | empty |
| 2 | 361 | 0.85 | 0.95 | 42 | empty |
| 3 | 1087 | 0.82 | 0.84 | 103 | NA, EDO |
| 4 | 1065 | 0.82 | 0.83 | 100 | NA, EDO |
| 5 | 108 | 0.79 | 0.99 | 24 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2932 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 2930 Ų buried · 64 hydrogen bonds · protein-protein
- D–F · 2915 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 2911 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 2903 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 4RU4 · Crystal structure of the tailspike protein gp49 from Pseudomonas phage LKA1 · 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 Q0E5W5
- Elsewhere: RCSB PDB 4RU4 · PDBe 4RU4 · UniProt Q0E5W5
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