SAXSdb — 3fnt

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

HAP protein

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Inhibitor, (IVA)VV(STA)A(STA) × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Inhibitor, (IVA)VV(STA)A(STA) × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IM15_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–332； UniProt 120–451

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	3fnt
Deposition date deposition_date	2008-12-26
Structure title title	Crystal structure of pepstatin A bound histo-aspartic protease (HAP) from Plasmodium falciparum
Keywords keywords	Histo-aspartic protease, HAP, Plasmepsin, Pepstatin A, Aspartic protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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.

3fnt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fnt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fnt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.32 Å
Rg (electron density)	20.11 Å
Total Rg	21.19 Å
Atom count	2626
Residues	326
Excluded volume	47286 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fnt__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fnt__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	HAP protein
Molecular weight formula_weight	37435.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2635

SYLGSEFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAKNL

Source Source

Source organism organism	Plasmodium falciparum
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Inhibitor, (IVA)VV(STA)A(STA)
Molecular weight formula_weight	685.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

XVVXAX

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3fntA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	3fntA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

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Unit-cell length a length_a	70.700 Å
Unit-cell length b length_b	70.700 Å
Unit-cell length c length_c	158.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2880
R_work r_work	0.2850
R_free r_free	0.3530

Crystal structure of pepstatin A bound histo-aspartic protease (HAP) from Plasmodium falciparum

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

HAP protein

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

3fnt__assembly_2__model_1

3fnt__assembly_2__model_1 | I(q)

3fnt__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of pepstatin A bound histo-aspartic protease (HAP) from Plasmodium falciparum

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

HAP protein

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

3fnt__assembly_2__model_1

3fnt__assembly_2__model_1 | I(q)

3fnt__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)