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Structural basis for substrate recognition and reaction mechanism of bacterial aminopeptidase peps
Analyse Structural basis for substrate recognition and reaction mechanism of bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ICR
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase peps
- EC
- 3.4.11.-
- UniProt
- Q97SP8
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminopeptidase peps (EC 3.4.11.-) | protein | 406 | 38% helix, 26% strand | Q97SP8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CAC · Cacodylate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.80 | 0.82 | 75 | empty |
| 2 | 423 | 0.59 | 0.75 | 48 | CAC |
| 3 | 340 | 0.57 | 0.76 | 43 | ZN, CAC |
| 4 | 149 | 0.51 | 0.79 | 29 | CAC |
| 5 | 117 | 0.49 | 0.80 | 25 | CAC |
Interfaces
1 interface between chains.
- A–B · 1565 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4ICR · Structural basis for substrate recognition and reaction mechanism of bacterial… · 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 Q97SP8
- Elsewhere: RCSB PDB 4ICR · PDBe 4ICR · UniProt Q97SP8
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