MolNFT v1 · #102343 · protein
Structural and kinetic bases for the metal preference of the M18 aminopeptidase from pseudomonas aeruginosa
4OIW · Probable M18 family aminopeptidase 2: “Structural and kinetic bases for the metal preference of the M18 aminopeptidase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 4OIW
- Type
- protein
- Length
- 2,448 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable M18 family aminopeptidase 2
- EC
- 3.4.11.-
- UniProt
- Q9HYZ3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Probable M18 family aminopeptidase 2 (EC 3.4.11.-) | protein | 408 | 28% helix, 29% strand | Q9HYZ3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 28 | empty |
| 2 | 848 | 0.76 | 0.80 | 97 | empty |
| 3 | 539 | 0.76 | 0.83 | 49 | empty |
| 4 | 542 | 0.75 | 0.82 | 46 | empty |
| 5 | 745 | 0.74 | 0.80 | 93 | empty |
Interfaces
7 interfaces between chains.
- C–E · 3322 Ų buried · 63 hydrogen bonds · protein-protein
- E–F · 1826 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1826 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 1819 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4OIW · Structural and kinetic bases for the metal preference of the M18 aminopeptidase from… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9HYZ3 · AlphaFold monomer V2.0 prediction for probable M18 family aminopeptidase 2 (Q9HYZ3) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9HYZ3
- Elsewhere: RCSB PDB 4OIW · PDBe 4OIW · UniProt Q9HYZ3
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