SAXSdb — 7dij

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

Falcilysin

Plasmodium falciparum 3D7

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 59–1193	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 3 EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 H8F 2-(aminomethyl)-3,5-ditert-butyl-phenol × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350	Resolution 1.90 Å R-free 0.206

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 7DIJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3S5H Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Deposited 2011-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1193（1193 aa）	Not recorded	CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；11% PEG6000,10%PEG400,0.1M ADA, 20mM Mg acetate,20 mM Co acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.257
3S5I Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Deposited 2011-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1193（1193 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；11% PEG6000, 10%PEG400, 0.1M ADA, 20mM Mg acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 1.74 Å R-free 0.197
3S5K Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Deposited 2011-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1193（1193 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；20% PEG6000, 0.1M MES, 5 M Zn acetate,0.1% - mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.316
3S5M Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Deposited 2011-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1193（1193 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；11% PEG6000, 10% PEG400, 0.1M ADA, 20 mM Mg acetate, 20 mM Zn acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.55 Å R-free 0.214
7DI7 Falcilysin in complex with chloroquine Deposited 2020-11-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–1193（1135 aa）	Not recorded	ACT ACETATE ION × 2 CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate trihydrate pH 8.0, 20% w/v PEG 3,350	Resolution 1.82 Å R-free 0.198
7DIA Falcilysin in complex with mefloquine Deposited 2020-11-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–1193（1135 aa）	Not recorded	H8O (S)-[2,8-bis(trifluoromethyl)quinolin-4-yl]-[(2S)-piperidin-2-yl]methanol × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 3 YMZ (11R,12S)- Mefloquine × 1 EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate trihydrate pH 7.0, 20% w/v PEG 3,350	Resolution 1.55 Å R-free 0.197
8HO4 Falcilysin in complex with MMV000848 Deposited 2022-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–1193（1135 aa）	Not recorded	XUH (2R)-1-(9H-carbazol-9-yl)-3-(cyclopentylamino)propan-2-ol × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.05 M Sodium HEPES, 0.05M MOPS pH 7.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20,000	Resolution 1.96 Å R-free 0.206
8HO5 Falcilysin in complex with MMV665806 Deposited 2022-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–1193（1135 aa）	Not recorded	XUN (2S)-1-(2,3-dimethyl-1H-indol-1-yl)-3-{[(1S,2S)-2-methylcyclohexyl]amino}propan-2-ol × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.039M Bicine, 0.061M TRIZMA base pH 8.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20,000	Resolution 2.00 Å R-free 0.189
8WXW Falcilysin in complex with hemoglobin alpha chain peptide Deposited 2023-10-30	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 59–1193（1135 aa）	Mutation：E132Q	GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；4% w/v PEG 1500, 20% v/v glycerol	Resolution 1.86 Å R-free 0.210
8WXZ Falcilysin in complex with hemoglobin beta chain peptide Deposited 2023-10-30	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 59–1193（1135 aa）	Mutation：E132Q	PEG DI(HYDROXYETHYL)ETHER × 1 ACY ACETIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.12M monosaccharides, 0.1M imidazole/MES monohydrate pH 6.5, 20% v/v PEG 500, 10% w/v PEG 20000	Resolution 2.30 Å R-free 0.251
8WYT Partially closed Falcilysin bound to MK-4815, from MK-4815-treated dataset Deposited 2023-10-31	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 59–1193（1135 aa）	Not recorded	H8F 2-(aminomethyl)-3,5-ditert-butyl-phenol × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8WYU Open Falcilysin, from MK-4815-treated dataset Deposited 2023-10-31	Different construct 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 61–1193（1133 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8WYX Partially closed falcilysin, from free falcilysin dataset Deposited 2023-10-31	Different construct 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 59–1192（1134 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8WYY Open falcilysin, from free falcilysin dataset Deposited 2023-10-31	Different construct 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 61–1193（1133 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FCLN_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–1158； UniProt 59–1193

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	7dij
Deposition date deposition_date	2020-11-19
Structure title title	Falcilysin in complex with MK-4815
Keywords keywords	PROTEIN BINDING-inhibitor complex; PROTEIN BINDING/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	31.30 Å
Radius of gyration Rg (electron density) rg_electron	30.02 Å
Forward intensity I(0) i0	234675000.00
Molecular weight molecular_weight	126090.0 kDa
Excluded volume excluded_volume	159600 Å³
Envelope volume envelope_volume	197220 Å³
Hydration-shell volume shell_volume	52226 Å³
Envelope diameter envelope_diameter	100.8 Å
Shell Rg shell_rg	39.18 Å
Envelope Rg envelope_rg	29.43 Å
Shape Rg shape_rg	30.00 Å
Total Rg total_rg	30.90 Å
Total atoms total_atoms	8893
Residues n_residues	1074
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	97.5 Å
Rg (real space) rg_real	31.01 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	2.3470e+08
I(0) uncertainty (real space) i0_real_error	3.1390e+06
Rg (reciprocal space) rg_reciprocal	31.13 Å
I(0) (reciprocal space) i0_reciprocal	234700000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.0 Å
Skewness Skewness skewness	0.007
Kurtosis Kurtosis kurtosis	-0.491
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	68510000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Falcilysin
Molecular weight formula_weight	135039.4 kDa
EC 编号 ec_number	3.4.24.-
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	9974

MHHHHHHSSGVDLGTENLYFQSMEWIHEKSPKHNSYDIIEKRYNEEFKMTYTVYQHKKAKTQVISLGTNDPLDVEQAFAFYVKTLTHSGKGIPHILEHSVLSGSKNYNYKNSIGLLEKGTLHTHLNAYTFNDRTVYMAGSMNNKDFFNIMGVYMDSVFQPNVLENKYIFETEGWTYEVEKLKEDEKGKAEIPQMKDYKVSFNGIVYNEMKGALSSPLEDLYHEEMKYMFPDNVHSNNSGGDPKEITNLTYEEFKEFYYKNYNPKKVKVFFFSKNNPTELLNFVDQYLGQLDYSKYRDDAVESVEYQTYKKGPFYIKKKYGDHSEEKENLVSVAWLLNPKVDKTNNHNNNHSNNQSSENNGYSNGSHSSDLSLENPTDYFVLLIINNLLIHTPESVLYKALTDCGLGNNVIDRGLNDSLVQYIFSIGLKGIKRNNEKIKNFDKVHYEVEDVIMNALKKVVKEGFNKSAVEASINNIEFILKEANLKTSKSIDFVFEMTSKLNYNRDPLLIFEFEKYLNIVKNKIKNEPMYLEKFVEKHFINNAHRSVILLEGDENYAQEQENLEKQELKKRIENFNEQEKEQVIKNFEELSKYKNAEESPEHLNKFPIISISDLNKKTLEVPVNVYFTNINENNNIMETYNKLKTNEHMLKDNMDVFLKKYVLKNDKHNTNNNNNNNNNMDYSFTETKYEGNVPILVYEMPTTGIVYLQFVFSLDHLTVDELAYLNLFKTLILENKTNKRSSEDFVILREKNIGSMSANVALYSKDDHLNVTDKYNAQALFNLEMHVLSHKCNDALNIALEAVKESDFSNKKKVIDILKRKINGMKTTFSEKGYAILMKYVKAHLNSKHYAHNIIYGYENYLKLQEQLELAENDFKTLENILVRIRNKIFNKKNLMVSVTSDYGALKHLFVNSNESLKNLVSYFEENDKYINDMQNKVNDPTVMGWNEEIKSKKLFDEEKVKKEFFVLPTFVNSVSMSGILFKPGEYLDPSFTVIVAALKNSYLWDTVRGLNGAYGVFADIEYDGSVVFLSARDPNLEKTLATFRESAKGLRKMADTMTENDLLRYIINTIGTIDKPRRGIELSKLSFLRLISNESEQDRVEFRKRIMNTKKEDFYKFADLLESKVNEFEKNIVIITTKEKANEYIANVDGEFKKVLIE

来源 Source

来源生物 organism	Plasmodium falciparum 3D7
NCBI Class编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-(aminomethyl)-3,5-ditert-butyl-phenol
Molecular weight formula_weight	235.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1017

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8. Citations (1)

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Unit-cell length a length_a	93.520 Å
Unit-cell length b length_b	105.830 Å
Unit-cell length c length_c	125.930 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	48.780 Å
R factor r_factor	0.1862
R_work r_work	0.1851
R_free r_free	0.2060

fit	/app/data/saxs_computation/di/7dij/7dij.fit
pddf	/app/data/pr_computation/di/7dij/7dij.pr.out
profile	/app/data/saxs_computation/di/7dij/7dij.dat

Falcilysin in complex with MK-4815

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

Falcilysin

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