SAXSdb — 2ghu

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

falcipain 2

Plasmodium falciparum

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 244–484	Fragment：Mature wild-type enzyme (residues 1-241)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.4-0.8 M ammonium sulfate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.274
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 244–484	Fragment：Mature wild-type enzyme (residues 1-241)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.4-0.8 M ammonium sulfate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.274
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 244–484	Fragment：Mature wild-type enzyme (residues 1-241)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.4-0.8 M ammonium sulfate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.274
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 244–484	Fragment：Mature wild-type enzyme (residues 1-241)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.4-0.8 M ammonium sulfate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.274

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 2GHU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YVB the Plasmodium falciparum Cysteine Protease Falcipain-2 Deposited 2005-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 244–484（241 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1 M HEPES pH 7.5 and 4.3 M NaCl , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.264
2OUL The Structure of Chagasin in Complex with a Cysteine Protease Clarifies the Binding Mode and Evolution of a New Inhibitor Family Deposited 2007-02-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 244–484（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；277 K；20% (v/v) PEG-300, 0.1 M Tris pH 8.5, 5% (w/v) PEG8000, and 10-15% (v/v) glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00	Resolution 2.20 Å R-free 0.232
3PNR Structure of PbICP-C in complex with falcipain-2 Deposited 2010-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 245–484（240 aa） Fragment：mature FP-2 (UNP residues 245-484)	Mutation：C285A	GOL GLYCEROL × 3 CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；200 mM sodium acetate, 27.5 mM CdCl2, 100 mM MES, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.60 Å R-free 0.229
6SSZ Structure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor. Deposited 2019-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–483（240 aa）	Mutation：C25A	JV1 (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% w/v PEG 4000. Crystal soaked for 2 hours with (E)-chalcone #48 inhibitor. Inhibitor prepared in 100% DMSO, 100 mM concentration and then diluted to 1 mM in mother liquor for crystal soaking.	Resolution 3.45 Å R-free 0.308
6SSZ Structure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor. Deposited 2019-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 244–483（240 aa）	Mutation：C25A	JV1 (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% w/v PEG 4000. Crystal soaked for 2 hours with (E)-chalcone #48 inhibitor. Inhibitor prepared in 100% DMSO, 100 mM concentration and then diluted to 1 mM in mother liquor for crystal soaking.	Resolution 3.45 Å R-free 0.308

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9N6S8_PLAFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 244–484 Author chain B； PDBConstruct 1–241； UniProt 244–484 Author chain C； PDBConstruct 1–241； UniProt 244–484 Author chain D； PDBConstruct 1–241； UniProt 244–484

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	2ghu
Deposition date deposition_date	2006-03-27
Structure title title	Crystal structure of falcipain-2 from Plasmodium falciparum
Keywords keywords	papain-like cysteine protease, L-domain, R-domain, alpha helix, random coil, twisted antiparallel beta-sheet, HYDROLASE; HYDROLASE
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	35.50 Å
Radius of gyration Rg (electron density) rg_electron	35.05 Å
Forward intensity I(0) i0	184131000.00
Molecular weight molecular_weight	108330.0 kDa
Excluded volume excluded_volume	134890 Å³
Envelope volume envelope_volume	174110 Å³
Hydration-shell volume shell_volume	41725 Å³
Envelope diameter envelope_diameter	116.3 Å
Shell Rg shell_rg	41.15 Å
Envelope Rg envelope_rg	34.64 Å
Shape Rg shape_rg	35.03 Å
Total Rg total_rg	35.54 Å
Total atoms total_atoms	7614
Residues n_residues	962
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	112.8 Å
Rg (real space) rg_real	35.41 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.8410e+08
I(0) uncertainty (real space) i0_real_error	3.2200e+06
Rg (reciprocal space) rg_reciprocal	35.47 Å
I(0) (reciprocal space) i0_reciprocal	184100000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.1 Å
Skewness Skewness skewness	0.125
Kurtosis Kurtosis kurtosis	-0.678
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34270000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.912

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ghua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d2ghub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d2ghuc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d2ghud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

CATH v4.4 (4 domains)

Domain ID domain_id	2ghuA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	2ghuB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	2ghuC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	2ghuD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	145.830 Å
Unit-cell length b length_b	168.280 Å
Unit-cell length c length_c	178.090 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2310
R_free r_free	0.2740

Description description	falcipain 2
Molecular weight formula_weight	27186.7 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7654

Crystal structure of falcipain-2 from Plasmodium falciparum

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

falcipain 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

fit	/app/data/saxs_computation/gh/2ghu/2ghu.fit
pddf	/app/data/pr_computation/gh/2ghu/2ghu.pr.out
profile	/app/data/saxs_computation/gh/2ghu/2ghu.dat