MolNFT v1 · #106267 · protein
Crystal structure of the pseudomonas phage PHI297 tailspike GP61
4RU5 · Tailspike GP27: “Crystal structure of the pseudomonas phage PHI297 tailspike GP61”. X-ray diffraction, 2 ligands (NA, CA), 17 pockets (best druggability 0.82). MolNFT v1 #106267 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4RU5
- Type
- protein
- Length
- 1,802 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tailspike GP27
- UniProt
- H2BD96
- Ligands
- NA, CA
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tailspike GP27 | protein | 600 | 4% helix, 46% strand | H2BD96 |
| C | Tailspike GP27 | protein | 602 | 4% helix, 45% strand | H2BD96 |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains A, B, C
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C
- ACT · Acetate ion · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.82 | 0.92 | 57 | empty |
| 2 | 577 | 0.76 | 0.84 | 66 | empty |
| 3 | 121 | 0.59 | 0.85 | 28 | empty |
| 4 | 160 | 0.55 | 0.81 | 30 | empty |
| 5 | 158 | 0.54 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3291 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3287 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 3249 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 4RU5 · Crystal Structure of the Pseudomonas phage phi297 tailspike gp61 · 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 H2BD96
- Elsewhere: RCSB PDB 4RU5 · PDBe 4RU5 · UniProt H2BD96
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