4k3n

Phosphonic Arginine Mimetics as Inhibitors of the M17 Aminopeptidases from Plasmodium falciparum

Method: X-RAY DIFFRACTION D_max: 210.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

M17 leucyl aminopeptidase

Plasmodium falciparum 3D7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 84–605 Chain B； UniProt 84–605 Chain C； UniProt 84–605 Chain D； UniProt 84–605 Chain E； UniProt 84–605 Chain F； UniProt 84–605	Fragment：unp residues 84-605 Mutation：D152N, D515N, D516N	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 1OT {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid × 6 SO4 SULFATE ION × 11 1PE PENTAETHYLENE GLYCOL × 15 2PE NONAETHYLENE GLYCOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris, 0.2M LiSO4, 1mM TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.240
2	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 84–605 Chain H； UniProt 84–605 Chain I； UniProt 84–605 Chain J； UniProt 84–605 Chain K； UniProt 84–605 Chain L； UniProt 84–605	Fragment：unp residues 84-605 Mutation：D152N, D515N, D516N	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 1OT {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid × 6 SO4 SULFATE ION × 10 1PE PENTAETHYLENE GLYCOL × 19 2PE NONAETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris, 0.2M LiSO4, 1mM TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.240

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4K3N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KQX Structure of a protease 1 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：residues 84-605 Chain B 84–605（522 aa） Fragment：residues 84-605 Chain C 84–605（522 aa） Fragment：residues 84-605 Chain D 84–605（522 aa） Fragment：residues 84-605 Chain E 84–605（522 aa） Fragment：residues 84-605 Chain F 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	ZN ZINC ION × 6 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 11 1PE PENTAETHYLENE GLYCOL × 24 2PE NONAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.01 Å R-free 0.232
3KQX Structure of a protease 1 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：residues 84-605 Chain H 84–605（522 aa） Fragment：residues 84-605 Chain I 84–605（522 aa） Fragment：residues 84-605 Chain J 84–605（522 aa） Fragment：residues 84-605 Chain K 84–605（522 aa） Fragment：residues 84-605 Chain L 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	ZN ZINC ION × 6 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 5 1PE PENTAETHYLENE GLYCOL × 30 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.01 Å R-free 0.232
3KQZ Structure of a protease 2 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：residues 84-605 Chain B 84–605（522 aa） Fragment：residues 84-605 Chain C 84–605（522 aa） Fragment：residues 84-605 Chain D 84–605（522 aa） Fragment：residues 84-605 Chain E 84–605（522 aa） Fragment：residues 84-605 Chain F 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 SO4 SULFATE ION × 16 1PE PENTAETHYLENE GLYCOL × 24 2PE NONAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.39 Å R-free 0.242
3KQZ Structure of a protease 2 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：residues 84-605 Chain H 84–605（522 aa） Fragment：residues 84-605 Chain I 84–605（522 aa） Fragment：residues 84-605 Chain J 84–605（522 aa） Fragment：residues 84-605 Chain K 84–605（522 aa） Fragment：residues 84-605 Chain L 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 SO4 SULFATE ION × 11 1PE PENTAETHYLENE GLYCOL × 29 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.39 Å R-free 0.242
3KR4 Structure of a protease 3 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：residues 84-605 Chain B 84–605（522 aa） Fragment：residues 84-605 Chain C 84–605（522 aa） Fragment：residues 84-605 Chain D 84–605（522 aa） Fragment：residues 84-605 Chain E 84–605（522 aa） Fragment：residues 84-605 Chain F 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 6 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 6 MG MAGNESIUM ION × 6 SO4 SULFATE ION × 8 1PE PENTAETHYLENE GLYCOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSo4, 1mM TCEP, 1mM MgCl2, 1mM Bestatin, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.242
3KR4 Structure of a protease 3 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：residues 84-605 Chain H 84–605（522 aa） Fragment：residues 84-605 Chain I 84–605（522 aa） Fragment：residues 84-605 Chain J 84–605（522 aa） Fragment：residues 84-605 Chain K 84–605（522 aa） Fragment：residues 84-605 Chain L 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 6 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 6 MG MAGNESIUM ION × 6 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSo4, 1mM TCEP, 1mM MgCl2, 1mM Bestatin, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.242
3KR5 Structure of a protease 4 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：residues 84-605 Chain B 84–605（522 aa） Fragment：residues 84-605 Chain C 84–605（522 aa） Fragment：residues 84-605 Chain D 84–605（522 aa） Fragment：residues 84-605 Chain E 84–605（522 aa） Fragment：residues 84-605 Chain F 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 BEY (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid × 6 SO4 SULFATE ION × 8 1PE PENTAETHYLENE GLYCOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, 1mM Co4/BEY, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.56 Å R-free 0.278
3KR5 Structure of a protease 4 Deposited 2009-11-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：residues 84-605 Chain H 84–605（522 aa） Fragment：residues 84-605 Chain I 84–605（522 aa） Fragment：residues 84-605 Chain J 84–605（522 aa） Fragment：residues 84-605 Chain K 84–605（522 aa） Fragment：residues 84-605 Chain L 84–605（522 aa） Fragment：residues 84-605	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 BEY (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid × 6 SO4 SULFATE ION × 7 1PE PENTAETHYLENE GLYCOL × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, 1mM ZnCl2, 1mM Co4/BEY, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.56 Å R-free 0.278
3T8W A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases Deposited 2011-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：UNP residues 84-605 Chain B 84–605（522 aa） Fragment：UNP residues 84-605 Chain C 84–605（522 aa） Fragment：UNP residues 84-605 Chain D 84–605（522 aa） Fragment：UNP residues 84-605 Chain E 84–605（522 aa） Fragment：UNP residues 84-605 Chain F 84–605（522 aa） Fragment：UNP residues 84-605	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 DGZ N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide × 6 SO4 SULFATE ION × 12 1PE PENTAETHYLENE GLYCOL × 14 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40%(v/v) PEG400, 0.1M Tris, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.200
3T8W A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases Deposited 2011-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：UNP residues 84-605 Chain H 84–605（522 aa） Fragment：UNP residues 84-605 Chain I 84–605（522 aa） Fragment：UNP residues 84-605 Chain J 84–605（522 aa） Fragment：UNP residues 84-605 Chain K 84–605（522 aa） Fragment：UNP residues 84-605 Chain L 84–605（522 aa） Fragment：UNP residues 84-605	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 DGZ N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide × 6 SO4 SULFATE ION × 17 1PE PENTAETHYLENE GLYCOL × 19 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40%(v/v) PEG400, 0.1M Tris, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.200
4R6T Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor Deposited 2014-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Chain B 84–605（522 aa） Chain C 84–605（522 aa） Chain D 84–605（522 aa） Chain E 84–605（522 aa） Chain F 84–605（522 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 12 R5T tert-butyl {(1S)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}carbamate × 6 1PE PENTAETHYLENE GLYCOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K	Resolution 2.60 Å R-free 0.269
4R6T Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor Deposited 2014-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Chain H 84–605（522 aa） Chain I 84–605（522 aa） Chain J 84–605（522 aa） Chain K 84–605（522 aa） Chain L 84–605（522 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 11 R5T tert-butyl {(1S)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}carbamate × 6 1PE PENTAETHYLENE GLYCOL × 8 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K	Resolution 2.60 Å R-free 0.269
4R7M Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor Deposited 2014-08-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Fragment：unp residues 84-605 Chain B 84–605（522 aa） Fragment：unp residues 84-605 Chain C 84–605（522 aa） Fragment：unp residues 84-605 Chain D 84–605（522 aa） Fragment：unp residues 84-605 Chain E 84–605（522 aa） Fragment：unp residues 84-605 Chain F 84–605（522 aa） Fragment：unp residues 84-605	Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 1PE PENTAETHYLENE GLYCOL × 7 3MW 4-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide × 6 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K	Resolution 2.85 Å R-free 0.291
4R7M Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor Deposited 2014-08-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Fragment：unp residues 84-605 Chain H 84–605（522 aa） Fragment：unp residues 84-605 Chain I 84–605（522 aa） Fragment：unp residues 84-605 Chain J 84–605（522 aa） Fragment：unp residues 84-605 Chain K 84–605（522 aa） Fragment：unp residues 84-605 Chain L 84–605（522 aa） Fragment：unp residues 84-605	Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N Mutation：D152N, D515N, D516N	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 1PE PENTAETHYLENE GLYCOL × 4 3MW 4-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide × 6 SO4 SULFATE ION × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K	Resolution 2.85 Å R-free 0.291
4X2T X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum Deposited 2014-11-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain B 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain C 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain D 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain E 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain F 85–603（519 aa） Fragment：UNP residues 85 to 603	Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q	ZN ZINC ION × 12 TOD (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid × 5 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 8 1PE PENTAETHYLENE GLYCOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；35% (v/v) PEG 400, 0.1 M Tris pH 8.6, 0.2 M Li2SO4	Resolution 2.73 Å R-free 0.274
4X2T X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum Deposited 2014-11-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain H 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain I 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain J 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain K 85–603（519 aa） Fragment：UNP residues 85 to 603 Chain L 85–603（519 aa） Fragment：UNP residues 85 to 603	Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q Mutation：N152Q, N515Q, N545Q	ZN ZINC ION × 12 TOD (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid × 6 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 5 1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；35% (v/v) PEG 400, 0.1 M Tris pH 8.6, 0.2 M Li2SO4	Resolution 2.73 Å R-free 0.274
7RIE Plasmodium falciparum M17 in complex with inhibitor MIPS2571 Deposited 2021-07-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 1PE PENTAETHYLENE GLYCOL × 5 5IF N-{(1R)-2-(hydroxyamino)-1-[4'-(hydroxymethyl)[1,1'-biphenyl]-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide × 6 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG400, 0.2M LiSO4, 0.1M Tris pH 7.5 to 8.8	Resolution 2.49 Å R-free 0.229
7RIE Plasmodium falciparum M17 in complex with inhibitor MIPS2571 Deposited 2021-07-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 85–605（521 aa） Chain H 85–605（521 aa） Chain I 85–605（521 aa） Chain J 85–605（521 aa） Chain K 85–605（521 aa） Chain L 85–605（521 aa）	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 1PE PENTAETHYLENE GLYCOL × 4 5IF N-{(1R)-2-(hydroxyamino)-1-[4'-(hydroxymethyl)[1,1'-biphenyl]-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG400, 0.2M LiSO4, 0.1M Tris pH 7.5 to 8.8	Resolution 2.49 Å R-free 0.229
7SRV Metal dependent activation of Plasmodium falciparum M17 aminopeptidase (inactive form), spacegroup P22121 Deposited 2021-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 ACT ACETATE ION × 8 CA CALCIUM ION × 12 EDO 1,2-ETHANEDIOL × 6 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20 % PEG3350, 0.2 M calcium acetate	Resolution 2.03 Å R-free 0.219
7T3V Metal dependent activation of Plasmodium falciparum M17 aminopeptidase, spacegroup P22121 after crystals soaked with Zn2+ Deposited 2021-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM HEPES pH 8.0, 150 mM NaCl	Resolution 2.30 Å R-free 0.264
8EZ4 Plasmodium falciparum M17 in complex with inhibitor 9aa Deposited 2022-10-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Not recorded	X10 N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide × 6 SO4 SULFATE ION × 7 1PE PENTAETHYLENE GLYCOL × 16 CO3 CARBONATE ION × 6 ZN ZINC ION × 12 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 1.89 Å R-free 0.216
8EZ4 Plasmodium falciparum M17 in complex with inhibitor 9aa Deposited 2022-10-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 85–605（521 aa） Chain H 85–605（521 aa） Chain I 85–605（521 aa） Chain J 85–605（521 aa） Chain K 85–605（521 aa） Chain L 85–605（521 aa）	Not recorded	X10 N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide × 6 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 14 CO3 CARBONATE ION × 6 ZN ZINC ION × 12 NA SODIUM ION × 5 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 1.89 Å R-free 0.216
8SVM Plasmodium falciparum M17 aminopeptidase bound to MMV1557817 Deposited 2023-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Chain B 84–605（522 aa） Chain C 84–605（522 aa） Chain D 84–605（522 aa） Chain E 84–605（522 aa） Chain F 84–605（522 aa）	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 WRC N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide × 6 1PE PENTAETHYLENE GLYCOL × 15 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4	Resolution 2.30 Å R-free 0.252
8SVM Plasmodium falciparum M17 aminopeptidase bound to MMV1557817 Deposited 2023-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Chain H 84–605（522 aa） Chain I 84–605（522 aa） Chain J 84–605（522 aa） Chain K 84–605（522 aa） Chain L 84–605（522 aa）	Not recorded	CO3 CARBONATE ION × 6 ZN ZINC ION × 12 WRC N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide × 6 1PE PENTAETHYLENE GLYCOL × 13 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4	Resolution 2.30 Å R-free 0.252
8SW9 Plasmodium falciparum M17 (A460S) mutant Deposited 2023-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 84–605（522 aa） Chain B 84–605（522 aa） Chain C 84–605（522 aa） Chain D 84–605（522 aa） Chain E 84–605（522 aa） Chain F 84–605（522 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 8 1PE PENTAETHYLENE GLYCOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4	Resolution 2.60 Å R-free 0.281
8SW9 Plasmodium falciparum M17 (A460S) mutant Deposited 2023-05-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 84–605（522 aa） Chain H 84–605（522 aa） Chain I 84–605（522 aa） Chain J 84–605（522 aa） Chain K 84–605（522 aa） Chain L 84–605（522 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 SO4 SULFATE ION × 9 1PE PENTAETHYLENE GLYCOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4	Resolution 2.60 Å R-free 0.281
9YC0 Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413) Deposited 2025-09-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 20 SO4 SULFATE ION × 29 A1CT4 N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 6 1PE PENTAETHYLENE GLYCOL × 16 DMS DIMETHYL SULFOXIDE × 7 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 2.37 Å R-free 0.271
9YC0 Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413) Deposited 2025-09-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 85–605（521 aa） Chain H 85–605（521 aa） Chain I 85–605（521 aa） Chain J 85–605（521 aa） Chain K 85–605（521 aa） Chain L 85–605（521 aa）	Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q Mutation：N152Q, N515Q, N546Q	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 16 SO4 SULFATE ION × 30 A1CT4 N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 5 1PE PENTAETHYLENE GLYCOL × 21 DMS DIMETHYL SULFOXIDE × 6 2PE NONAETHYLENE GLYCOL × 1 A1CT5 N-[(1S)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 2.37 Å R-free 0.271
9YC7 Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3k (MIPS3415) Deposited 2025-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 85–605（521 aa） Chain B 85–605（521 aa） Chain C 85–605（521 aa） Chain D 85–605（521 aa） Chain E 85–605（521 aa） Chain F 85–605（521 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 23 DMS DIMETHYL SULFOXIDE × 10 SO4 SULFATE ION × 12 GOL GLYCEROL × 1 A1CTH N-[(1R)-2-(hydroxyamino)-2-oxo-1-(quinolin-7-yl)ethyl]-3,3-dimethylbutanamide × 1 1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 2.37 Å R-free 0.287
9YC7 Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3k (MIPS3415) Deposited 2025-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 85–605（521 aa） Chain H 85–605（521 aa） Chain I 85–605（521 aa） Chain J 85–605（521 aa） Chain K 85–605（521 aa） Chain L 85–605（521 aa）	Not recorded	ZN ZINC ION × 12 CO3 CARBONATE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 20 DMS DIMETHYL SULFOXIDE × 9 SO4 SULFATE ION × 11 GOL GLYCEROL × 1 1PE PENTAETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30-40% PEG400, 0.1 M Tris pH 7.5-8.5, 0.2 M Li2SO4	Resolution 2.37 Å R-free 0.287

16 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8IL11_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–522； UniProt 84–605 Author chain B； PDBConstruct 1–522； UniProt 84–605 Author chain C； PDBConstruct 1–522； UniProt 84–605 Author chain D； PDBConstruct 1–522； UniProt 84–605 Author chain E； PDBConstruct 1–522； UniProt 84–605 Author chain F； PDBConstruct 1–522； UniProt 84–605 Author chain G； PDBConstruct 1–522； UniProt 84–605 Author chain H； PDBConstruct 1–522； UniProt 84–605 Author chain I； PDBConstruct 1–522； UniProt 84–605 Author chain J； PDBConstruct 1–522； UniProt 84–605 Author chain K； PDBConstruct 1–522； UniProt 84–605 Author chain L； PDBConstruct 1–522； UniProt 84–605

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4k3n
Deposition date deposition_date	2013-04-11
Structure title title	Phosphonic Arginine Mimetics as Inhibitors of the M17 Aminopeptidases from Plasmodium falciparum
Keywords keywords	Aminopeptidase, Leucyl aminopeptidase, Protease, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	71.28 Å
Radius of gyration Rg (electron density) rg_electron	71.53 Å
Forward intensity I(0) i0	6163170000.00
Molecular weight molecular_weight	684320.0 kDa
Excluded volume excluded_volume	862270 Å³
Envelope volume envelope_volume	1164900 Å³
Hydration-shell volume shell_volume	134160 Å³
Envelope diameter envelope_diameter	246.9 Å
Shell Rg shell_rg	70.37 Å
Envelope Rg envelope_rg	70.29 Å
Shape Rg shape_rg	71.56 Å
Total Rg total_rg	71.40 Å
Total atoms total_atoms	48055
Residues n_residues	6178
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	210.0 Å
Rg (real space) rg_real	71.16 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	6.1450e+09
I(0) uncertainty (real space) i0_real_error	1.3520e+08
Rg (reciprocal space) rg_reciprocal	70.08 Å
I(0) (reciprocal space) i0_reciprocal	6145000000.0000
Solution quality estimate total_estimate	0.8070
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.3 Å
Skewness Skewness skewness	0.389
Kurtosis Kurtosis kurtosis	-0.721
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0180
Highest regularization parameter α highest_alpha	1804000000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.001

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	M17 leucyl aminopeptidase
Molecular weight formula_weight	58709.0 kDa
Mutation mutation	D152N, D515N, D516N
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	49847

MASEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNNPGKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNSVAVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNLFRFFLETLFYEYMTDERFKSTDKNVNMEYIKHLGVYINNADTYKEEVEKARVYYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELEELKMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYNLKAAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMVSKNSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDIATLTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYRATLNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFKARKPKGFGVRLLTEFVLNDALHHHHHH

来源 Source

来源生物 organism	Plasmodium falciparum 3D7
NCBI Class编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	{(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid
Molecular weight formula_weight	253.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	34

Entity 7 Entity 7 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1784

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7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	4k3nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	4k3nL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	4k3nL02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

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8. Citations (1)

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Unit-cell length a length_a	173.716 Å
Unit-cell length b length_b	177.079 Å
Unit-cell length c length_c	229.185 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	45.106 Å
R factor r_factor	0.1986
R_work r_work	0.1964
R_free r_free	0.2401

fit	/app/data/saxs_computation/k3/4k3n/4k3n.fit
pddf	/app/data/pr_computation/k3/4k3n/4k3n.pr.out
profile	/app/data/saxs_computation/k3/4k3n/4k3n.dat