MolNFT v1 · #105470 · protein
Structure of the M1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
4R5X · M1 family aminopeptidase: “Structure of the M1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor”. X-ray diffraction, 3 ligands (R5X, ZN, MG), 13 pockets (best druggability 0.80). MolNFT v1 #105470…
- PDB
- 4R5X
- Type
- protein
- Length
- 888 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- R5X, ZN, MG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 888 | 46% helix, 22% strand | O96935 |
Ligands and binding sites
- R5X · 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.80 | 0.87 | 69 | GOL, R5X, DMS |
| 2 | 441 | 0.77 | 0.86 | 56 | DMS |
| 3 | 78 | 0.66 | 0.92 | 22 | empty |
| 4 | 147 | 0.59 | 0.84 | 25 | DMS |
| 5 | 52 | 0.58 | 0.91 | 18 | empty |
Compared structures
- 4R5X · Structure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic… · the same entry in another collection · chain A against A, TM-score 1.00
- O96935 · AlphaFold monomer V2.0 prediction for M1 family aminopeptidase (O96935) · a predicted model of the same protein · 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 O96935
- Elsewhere: RCSB PDB 4R5X · PDBe 4R5X · UniProt O96935
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