Download MendeleyCrystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide
Marapaka, A.K., Addlagatta, A.To be published.
5Y1S
Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide
- PDB DOI: https://doi.org/10.2210/pdb5Y1S/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Plasmodium falciparum FcB1/Columbia
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-07-21 Released: 2018-08-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.201
- R-Value Work: 0.167
- R-Value Observed: 0.168
Starting Model: experimental
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This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| M1 family aminopeptidase | 914 | Plasmodium falciparum FcB1/Columbia | Mutation(s): 0 EC: 3.4.11 |  | |
UniProt | |||||
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Explore O96935 Go to UniProtKB: O96935 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O96935 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| E8R Query on E8R | G [auth A] | (2R)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide C16 H25 N3 O3 OPDKYCNMBLFHGN-CQSZACIVSA-N |  | ||
| E8F Query on E8F | F [auth A] | (2S)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide C16 H25 N3 O3 OPDKYCNMBLFHGN-AWEZNQCLSA-N |  | ||
| GOL Query on GOL | H [auth A], I [auth A], J [auth A], K [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A], D [auth A], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.201
- R-Value Work: 0.167
- R-Value Observed: 0.168
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.699 | α = 90 |
| b = 109.405 | β = 90 |
| c = 112.991 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data collection |
| SCALEPACK | data scaling |
| MOLREP | model building |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
Entry History
Deposition Data
- Released Date: 2018-08-01 Deposition Author(s): Marapaka, A.K., Zhang, Y., Addlagatta, A.
Revision History (Full details and data files)
- Version 1.0: 2018-08-01
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
