MolNFT v1 · #101193 · protein
Structural and kinetic bases for the metal preference of the M18 aminopeptidase from pseudomonas aeruginosa
4NJQ · Probable M18 family aminopeptidase 2: “Structural and kinetic bases for the metal preference of the M18 aminopeptidase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (CO, CO3), 20 pockets (best druggability 0.81). MolNFT…
- 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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