Research workbench
Structural and kinetic bases for the metal preference of the M18 aminopeptidase from pseudomonas aeruginosa
Analyse Structural and kinetic bases for the metal preference of the M18 aminopeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NJQ
- Type
- protein
- Length
- 1,633 residues
- Chains
- 4
- 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
- CO, CO3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable M18 family aminopeptidase 2 (EC 3.4.11.-) | protein | 407 | 29% helix, 29% strand | Q9HYZ3 |
| B | Probable M18 family aminopeptidase 2 (EC 3.4.11.-) | protein | 410 | 28% helix, 29% strand | Q9HYZ3 |
| D | Probable M18 family aminopeptidase 2 (EC 3.4.11.-) | protein | 409 | 28% helix, 30% strand | Q9HYZ3 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · 4 copies · chains A, D, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.81 | 0.83 | 126 | CO3 |
| 2 | 96 | 0.78 | 0.98 | 28 | empty |
| 3 | 64 | 0.71 | 0.97 | 29 | empty |
| 4 | 228 | 0.67 | 0.85 | 38 | empty |
| 5 | 207 | 0.62 | 0.83 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–D · 3370 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1705 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1598 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4NJQ · Structural and kinetic bases for the metal preference of the M18 aminopeptidase from… · the same entry in another collection · chain D against D, 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 C 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 Q9HYZ3
- Elsewhere: RCSB PDB 4NJQ · PDBe 4NJQ · UniProt Q9HYZ3
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