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Structure and catalysis of acylaminoacyl peptidase
Analyse Structure and catalysis of acylaminoacyl peptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O4J
- Type
- protein
- Length
- 2,307 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylamino-acid-releasing enzyme
- EC
- 3.4.19.1
- UniProt
- Q9YBQ2
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 578 | 21% helix, 40% strand | Q9YBQ2 |
| B | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 574 | 22% helix, 40% strand | Q9YBQ2 |
| C | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 579 | 22% helix, 41% strand | Q9YBQ2 |
| D | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 576 | 21% helix, 40% strand | Q9YBQ2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.79 | 0.81 | 112 | GOL |
| 2 | 218 | 0.75 | 0.89 | 31 | GOL |
| 3 | 212 | 0.73 | 0.89 | 29 | GOL |
| 4 | 923 | 0.72 | 0.76 | 93 | GOL |
| 5 | 537 | 0.71 | 0.80 | 48 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1336 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1282 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 550 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q9YBQ2
- Elsewhere: RCSB PDB 3O4J · PDBe 3O4J · UniProt Q9YBQ2
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