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The structure of pseudomonas aeruginosa aminopeptidase pepp
Analyse The structure of pseudomonas aeruginosa aminopeptidase pepp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WZE
- Type
- protein
- Length
- 1,777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase P
- UniProt
- Q9HTW6
- Ligands
- PRO, ALA, MN, CA, NA, SO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aminopeptidase P | protein | 442 | 39% helix, 19% strand | Q9HTW6 |
| B | Aminopeptidase P | protein | 449 | 40% helix, 19% strand | Q9HTW6 |
| D | Aminopeptidase P | protein | 444 | 41% helix, 18% strand | Q9HTW6 |
Ligands and binding sites
- PRO · Proline · ligand · 4 copies · chains A, C, B, D
- ALA · Alanine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, D, C
- GOL · Glycerol · additive · 4 copies · chains A, C, D, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.87 | 0.88 | 129 | PRO, MN |
| 2 | 1075 | 0.86 | 0.87 | 116 | MN, PRO |
| 3 | 459 | 0.68 | 0.79 | 64 | NA |
| 4 | 222 | 0.63 | 0.82 | 37 | empty |
| 5 | 219 | 0.63 | 0.82 | 36 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2179 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2169 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 304 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 301 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WZE · The structure of Pseudomonas aeruginosa aminopeptidase PepP · 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 Q9HTW6
- Elsewhere: RCSB PDB 5WZE · PDBe 5WZE · UniProt Q9HTW6
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