SAXSdb — 1yvb

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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 244–484	Not recorded	Cystatin × 1 （P01038） 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

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 1YVB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GHU Crystal structure of falcipain-2 from Plasmodium falciparum Deposited 2006-03-27	Different construct 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 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 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 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 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
3PNR Structure of PbICP-C in complex with falcipain-2 Deposited 2010-11-19	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 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 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 1–241； UniProt 244–484

Cystatin

OrganismNot specified

UniProt P01038

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 I； UniProt 29–139	Not recorded	falcipain 2 × 1 （Q9N6S8） 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

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 1YVB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A67 CHICKEN EGG WHITE CYSTATIN WILDTYPE, NMR, 16 STRUCTURES Deposited 1998-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–139（108 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；303 K	Resolution not provided
1A90 RECOMBINANT MUTANT CHICKEN EGG WHITE CYSTATIN, NMR, 31 STRUCTURES Deposited 1998-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–116（108 aa）	Mutation：M29I, M89L	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CEW THE 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF CHICKEN EGG WHITE CYSTATIN AND ITS POSSIBLE MODE OF INTERACTION WITH CYSTEINE PROTEINASES Deposited 1993-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 32–139（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYT_CHICK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–111； UniProt 29–139

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	1yvb
Deposition date deposition_date	2005-02-15
Structure title title	the Plasmodium falciparum Cysteine Protease Falcipain-2
Keywords keywords	cysteine protease-inhibitor complex, 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	24.68 Å
Radius of gyration Rg (electron density) rg_electron	24.00 Å
Forward intensity I(0) i0	27549200.00
Molecular weight molecular_weight	39814.0 kDa
Excluded volume excluded_volume	49616 Å³
Envelope volume envelope_volume	60344 Å³
Hydration-shell volume shell_volume	22443 Å³
Envelope diameter envelope_diameter	92.5 Å
Shell Rg shell_rg	29.26 Å
Envelope Rg envelope_rg	24.61 Å
Shape Rg shape_rg	23.96 Å
Total Rg total_rg	24.77 Å
Total atoms total_atoms	2795
Residues n_residues	320
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	88.2 Å
Rg (real space) rg_real	24.90 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	2.7550e+07
I(0) uncertainty (real space) i0_real_error	3.6050e+05
Rg (reciprocal space) rg_reciprocal	24.85 Å
I(0) (reciprocal space) i0_reciprocal	27550000.0000
Solution quality estimate total_estimate	0.7391
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.548
Kurtosis Kurtosis kurtosis	-0.200
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7025000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.679; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2809

QMNYEEVIKKYRGEENFDHAAYDWRLHSGVTPVKDQKNCGSCWAFSSIGSVESQYAIRKNKLITLSEQELVDCSFKNYGCNGGLINNAFEDMIELGGICPDGDYPYVSDAPNLCNIDRCTEKYGIKNYLSVPDNKLKEALRFLGPISISVAVSDDFAFYKEGIFDGECGDQLNHAVMLVGFGMKEIVNPLTKKGEKHYYYIIKNSWGQQWGERGFINIETDESGLMRKCGLGTDAFIPLIE

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Cystatin
Molecular weight formula_weight	12588.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

RLLGAPVPVDENDEGLQRALQFAMAEYNRASNDKYSSRVVRVISAKRQLVSGIKYILQVEIGRTTCPKSSGDLQSCEFHDEPEMAKYTTCTFVVYSIPWLNQIKLLESKCQ

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yvba1
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	d1yvbi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

CATH v4.4 (2 domains)

Domain ID domain_id	1yvbA00
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	1yvbI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	96.036 Å
Unit-cell length b length_b	96.036 Å
Unit-cell length c length_c	124.164 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2322
R_work r_work	0.2322
R_free r_free	0.2641

fit	/app/data/saxs_computation/yv/1yvb/1yvb.fit
pddf	/app/data/pr_computation/yv/1yvb/1yvb.pr.out
profile	/app/data/saxs_computation/yv/1yvb/1yvb.dat

the Plasmodium falciparum Cysteine Protease 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

Cystatin

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)