9yc0

Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)

Method: X-RAY DIFFRACTION

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

M17 leucyl aminopeptidase

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 CARBONATE ION × 6 DI(HYDROXYETHYL)ETHER × 20 SULFATE ION × 29 N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 6 PENTAETHYLENE GLYCOL × 16 DIMETHYL SULFOXIDE × 7 NONAETHYLENE GLYCOL × 1 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 CARBONATE ION × 6 DI(HYDROXYETHYL)ETHER × 16 SULFATE ION × 30 N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 5 PENTAETHYLENE GLYCOL × 21 DIMETHYL SULFOXIDE × 6 NONAETHYLENE GLYCOL × 1 N-[(1S)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IL11_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–521； UniProt 85–605 Author chain B； PDBConstruct 1–521； UniProt 85–605 Author chain C； PDBConstruct 1–521； UniProt 85–605 Author chain D； PDBConstruct 1–521； UniProt 85–605 Author chain E； PDBConstruct 1–521； UniProt 85–605 Author chain F； PDBConstruct 1–521； UniProt 85–605 Author chain G； PDBConstruct 1–521； UniProt 85–605 Author chain H； PDBConstruct 1–521； UniProt 85–605 Author chain I； PDBConstruct 1–521； UniProt 85–605 Author chain J； PDBConstruct 1–521； UniProt 85–605 Author chain K； PDBConstruct 1–521； UniProt 85–605 Author chain L； PDBConstruct 1–521； UniProt 85–605

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yc0
Deposition date deposition_date	2025-09-17
Structure title title	Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)
Keywords keywords	M17 aminopeptidase, aminopeptidase inhibitor, P. falciparum, malaria, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9yc0__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9yc0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yc0__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.33 Å
Rg (electron density)	42.72 Å
Total Rg	42.95 Å
Atom count	24170
Residues	3085
Excluded volume	432690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yc0__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9yc0__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	M17 leucyl aminopeptidase
Molecular weight formula_weight	58577.8 kDa
EC 编号 ec_number	3.4.11.1
Mutation mutation	N152Q, N515Q, N546Q
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	51849

ASEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNNPGKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNSVAVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNLFRFFLETLFYEYMTDERFKSTDKNVNMEYIKHLGVYINNADTYKEEVEKARVYYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELEELKMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYNLKAAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMVSKNSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDIATLTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYRATLNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFKARKPKGFGVRLLTEFVLNDALHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism 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	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	nat
Copy count entity_count	36

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	59

Entity 6 Entity 6 non-polymer

Description description	N-[(1R)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide
Molecular weight formula_weight	321.4 kDa
Source method src_method	nat
Copy count entity_count	11

Entity 7 Entity 7 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	37

Entity 8 Entity 8 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 9 Entity 9 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	N-[(1S)-1-(1,3-benzothiazol-5-yl)-2-(hydroxyamino)-2-oxoethyl]-3,3-dimethylbutanamide
Molecular weight formula_weight	321.4 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3492

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Unit-cell length a length_a	173.729 Å
Unit-cell length b length_b	176.510 Å
Unit-cell length c length_c	231.308 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	orthorhombic

Resolution resolution	2.370 Å
Low-resolution limit resolution_low	48.420 Å
R factor r_factor	0.2212
R_work r_work	0.2185
R_free r_free	0.2708

Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)

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

M17 leucyl aminopeptidase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yc0__assembly_1__model_1

9yc0__assembly_1__model_1 | I(q)

9yc0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)

Plasmodium falciparum M17 aminopeptidase (PfA-M17) bound to inhibitor 3ab (MIPS3413)

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

M17 leucyl aminopeptidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yc0__assembly_1__model_1

9yc0__assembly_1__model_1 | I(q)

9yc0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)