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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
- 7ESP
- Type
- protein
- Length
- 2,091 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging NTPase
- UniProt
- A0A1U9AK63
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Packaging NTPase | protein | 265 | 34% helix, 22% strand | A0A1U9AK63 |
| B | Packaging NTPase | protein | 260 | 34% helix, 20% strand | A0A1U9AK63 |
| C | Packaging NTPase | protein | 263 | 35% helix, 22% strand | A0A1U9AK63 |
| D | Packaging NTPase | protein | 259 | 33% helix, 20% strand | A0A1U9AK63 |
| E | Packaging NTPase | protein | 265 | 32% helix, 22% strand | A0A1U9AK63 |
| F | Packaging NTPase | protein | 258 | 34% helix, 20% strand | A0A1U9AK63 |
| G | Packaging NTPase | protein | 263 | 34% helix, 22% strand | A0A1U9AK63 |
| H | Packaging NTPase | protein | 258 | 35% helix, 20% strand | A0A1U9AK63 |
Ligands and binding sites
- TAR · D(-)-tartaric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.79 | 0.81 | 92 | empty |
| 2 | 1023 | 0.79 | 0.80 | 121 | empty |
| 3 | 593 | 0.69 | 0.78 | 73 | TAR |
| 4 | 214 | 0.66 | 0.85 | 34 | TAR |
| 5 | 286 | 0.66 | 0.82 | 41 | TAR |
Interfaces
8 interfaces between chains.
- E–F · 1582 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1566 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1561 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1538 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7ESP · 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 7ESP · PDBe 7ESP · UniProt A0A1U9AK63
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