Research workbench
Structure and mutation analysis of the hexameric P4 from pseudomonas aeruginosa phage phiyy
Analyse Structure and mutation analysis of the hexameric P4 from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ESQ
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging NTPase
- UniProt
- A0A1U9AK63
- Ligands
- PPV, MG
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Packaging NTPase | protein | 264 | 33% helix, 22% strand | A0A1U9AK63 |
| B | Packaging NTPase | protein | 264 | 33% helix, 22% strand | A0A1U9AK63 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.65 | 0.79 | 46 | empty |
| 2 | 168 | 0.62 | 0.85 | 32 | MG, PPV |
| 3 | 292 | 0.62 | 0.80 | 38 | empty |
| 4 | 209 | 0.52 | 0.77 | 31 | empty |
| 5 | 74 | 0.39 | 0.79 | 20 | MG, PPV |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7ESQ · Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage… · 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 A0A1U9AK63
- Elsewhere: RCSB PDB 7ESQ · PDBe 7ESQ · UniProt A0A1U9AK63
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