SAXSdb — 3pnr

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 245–484	Fragment：mature FP-2 (UNP residues 245-484) Mutation：C285A	PbICP-C × 1 （Q4YW59） 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

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 3PNR	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 mutation/modification 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
2GHU Crystal structure of falcipain-2 from Plasmodium falciparum Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–484（241 aa） Fragment：Mature wild-type enzyme (residues 1-241)	Not recorded	No recorded non-water small molecule	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
2GHU Crystal structure of falcipain-2 from Plasmodium falciparum Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 244–484（241 aa） Fragment：Mature wild-type enzyme (residues 1-241)	Not recorded	No recorded non-water small molecule	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
2GHU Crystal structure of falcipain-2 from Plasmodium falciparum Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 244–484（241 aa） Fragment：Mature wild-type enzyme (residues 1-241)	Not recorded	No recorded non-water small molecule	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
2GHU Crystal structure of falcipain-2 from Plasmodium falciparum Deposited 2006-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 244–484（241 aa） Fragment：Mature wild-type enzyme (residues 1-241)	Not recorded	No recorded non-water small molecule	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
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 mutation/modification 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	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
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 oligomeric state 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 oligomeric state 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 8 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 1–240； UniProt 245–484

PbICP-C

Plasmodium berghei

UniProt Q4YW59

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 189–353	Fragment：UNP residues 189-353	Falcipain 2 × 1 （Q9N6S8） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q4YW59_PLABE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 23–187； UniProt 189–353

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	3pnr
Deposition date deposition_date	2010-11-19
Structure title title	Structure of PbICP-C in complex with falcipain-2
Keywords keywords	Immunoglobulin fold, 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	23.60 Å
Radius of gyration Rg (electron density) rg_electron	23.18 Å
Forward intensity I(0) i0	29722600.00
Molecular weight molecular_weight	41924.0 kDa
Excluded volume excluded_volume	52424 Å³
Envelope volume envelope_volume	62095 Å³
Hydration-shell volume shell_volume	23271 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	29.36 Å
Envelope Rg envelope_rg	23.60 Å
Shape Rg shape_rg	23.15 Å
Total Rg total_rg	24.06 Å
Total atoms total_atoms	2936
Residues n_residues	369
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	80.2 Å
Rg (real space) rg_real	23.69 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	2.9720e+07
I(0) uncertainty (real space) i0_real_error	3.8430e+05
Rg (reciprocal space) rg_reciprocal	23.67 Å
I(0) (reciprocal space) i0_reciprocal	29720000.0000
Solution quality estimate total_estimate	0.7843
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.211
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10100000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Falcipain 2
Molecular weight formula_weight	27026.5 kDa
Mutation mutation	C285A
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	2990

MNYEEVIKKYRGEENFDHAAYDWRLHSGVTPVKDQKNCGSAWAFSSIGSVESQYAIRKNKLITLSEQELVDCSFKNYGCNGGLINNAFEDMIELGGICPDGDYPYVSDAPNLCNIDRCTEKYGIKNYLSVPDNKLKEALRFLGPISISVAVSDDFAFYKEGIFDGECGDQLNHAVMLVGFGMKEIVNPLTKKGEKHYYYIIKNSWGQQWGERGFINIETDESGLMRKCGLGTDAFIPLIE

来源 Source

来源生物 organism	Plasmodium falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PbICP-C
Molecular weight formula_weight	21244.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGHHHHHHHHHHSSGHIEGRHMGDEKCGKSLKLGNISNQTNQETITQSLSVGEILCIDLEGNAGTGYLWVLLGIHKDEPIINPENFPTKLTKKSFFSEEISVTQPKKYKIDEHDSSKNVNREIESPEQKESDSKPKKPQMQLLGGPDRMRSVIKGHKPGKYYIVYSYYRPFSPTSGANTKIIYVTVQ

来源 Source

来源生物 organism	Plasmodium berghei
NCBI Class编号 ncbi_taxonomy_id	5821
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3pnra_
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 (2 domains)

Domain ID domain_id	3pnrA00
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	3pnrB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2020 —

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8. Citations (1)

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Unit-cell length a length_a	71.150 Å
Unit-cell length b length_b	71.150 Å
Unit-cell length c length_c	120.090 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	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	34.887 Å
R factor r_factor	0.1833
R_work r_work	0.1808
R_free r_free	0.2292

fit	/app/data/saxs_computation/pn/3pnr/3pnr.fit
pddf	/app/data/pr_computation/pn/3pnr/3pnr.pr.out
profile	/app/data/saxs_computation/pn/3pnr/3pnr.dat

Structure of PbICP-C in complex with falcipain-2

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

PbICP-C

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)