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9ekd

Structure of a C1r Zymogen Fragment Bound to SALO

Method: X-RAY DIFFRACTION Dmax: 148.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Salivary anti-complement protein

Lutzomyia longipalpis

UniProt Q5WPZ4

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 23–115 Non-standard monomer：Yes (specific site not provided by mmCIF) Complement C1r subcomponent × 1 （P00736） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M BIS-TRIS (pH 5.6), 0.2 M ammonium sulfate, 20% (w/v) PEG-3350 Resolution 3.28 Å R-free 0.286
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 23–115 Non-standard monomer：Yes (specific site not provided by mmCIF) Complement C1r subcomponent × 1 （P00736） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M BIS-TRIS (pH 5.6), 0.2 M ammonium sulfate, 20% (w/v) PEG-3350 Resolution 3.28 Å R-free 0.286

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 9EKD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5KX4 Structure of SALO Deposited 2016-07-20 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–115（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.02M calcium chloride, 30% v/v MPD and 0.1 M sodium acetate pH 4.6.
Resolution 1.94 Å R-free 0.189
5KX4 Structure of SALO Deposited 2016-07-20 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–115（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.02M calcium chloride, 30% v/v MPD and 0.1 M sodium acetate pH 4.6.
Resolution 1.94 Å R-free 0.189
5KX4 Structure of SALO Deposited 2016-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–115（93 aa）
Chain B 23–115（93 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.02M calcium chloride, 30% v/v MPD and 0.1 M sodium acetate pH 4.6.
Resolution 1.94 Å R-free 0.189
9EKE Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant Deposited 2024-12-02 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–115（93 aa）
Mutation：Y51F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic (pH 7.0), 20% (w/v) PEG-3350
Resolution 3.10 Å R-free 0.278
9EKE Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant Deposited 2024-12-02 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–115（93 aa）
Mutation：Y51F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic (pH 7.0), 20% (w/v) PEG-3350
Resolution 3.10 Å R-free 0.278

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

View Construct and Data Evidence
UniProt name SALO_LUTLO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–93； UniProt 23–115 Author chain B； PDBConstruct 1–93； UniProt 23–115

Complement C1r subcomponent

Homo sapiens

UniProt P00736

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 C； UniProt 308–705 Fragment：residues 308-705 Mutation：S654A Salivary anti-complement protein × 1 （Q5WPZ4） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M BIS-TRIS (pH 5.6), 0.2 M ammonium sulfate, 20% (w/v) PEG-3350 Resolution 3.28 Å R-free 0.286
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 308–705 Fragment：residues 308-705 Mutation：S654A Salivary anti-complement protein × 1 （Q5WPZ4） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M BIS-TRIS (pH 5.6), 0.2 M ammonium sulfate, 20% (w/v) PEG-3350 Resolution 3.28 Å R-free 0.286

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 9EKD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1APQ STRUCTURE OF THE EGF-LIKE MODULE OF HUMAN C1R, NMR, 19 STRUCTURES Deposited 1997-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 140–192（53 aa） Fragment：EGF-LIKE MODULE
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；288 K
Resolution not provided
1GPZ THE CRYSTAL STRUCTURE OF THE ZYMOGEN CATALYTIC DOMAIN OF COMPLEMENT PROTEASE C1R Deposited 2001-11-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 307–705（399 aa） Fragment：CATALYTIC DOMAIN OF HUMAN C1R, RESIDUES 307-705
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；1.5 M AMMONIUM SULFATE, 0.1M TAPS, PH 8.5, AT 20 DEG C.
Resolution 2.90 Å R-free 0.290
1GPZ THE CRYSTAL STRUCTURE OF THE ZYMOGEN CATALYTIC DOMAIN OF COMPLEMENT PROTEASE C1R Deposited 2001-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 307–705（399 aa） Fragment：CATALYTIC DOMAIN OF HUMAN C1R, RESIDUES 307-705
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；1.5 M AMMONIUM SULFATE, 0.1M TAPS, PH 8.5, AT 20 DEG C.
Resolution 2.90 Å R-free 0.290
1MD7 Monomeric structure of the zymogen of complement protease C1r Deposited 2002-08-07 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 375–702（328 aa） Fragment：C-terminal CCP-SP domain
Mutation：S637A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；ammonium sulfate, TAPS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.285
1MD8 Monomeric structure of the active catalytic domain of complement protease C1r Deposited 2002-08-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 375–703（329 aa） Fragment：C-terminal CCP-SP domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；ammonium sulfate, TAPS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.269
2QY0 Active dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts Deposited 2007-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 309–463（155 aa） Fragment：Sushi-1 and Sushi-2 domains, CCP1-CCP2
Chain B 464–705（242 aa） Fragment：Peptidase S1 domain
Chain C 309–463（155 aa） Fragment：Sushi-1 and Sushi-2 domains, CCP1-CCP2
Chain D 464–705（242 aa） Fragment：Peptidase S1 domain
Not recorded GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；288 K；14% (w/v) PEG 6000, 0.2 M NaCl, 10% (v/v) glycerol, 0.1 M Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.60 Å R-free 0.259
6F1C C1rC1s complex Deposited 2017-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 18–308（291 aa）
Chain C 18–308（291 aa）
Not recorded CA CALCIUM ION × 12 NA SODIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.20 Å R-free 0.305
6F1D CUB2 domain of C1r Deposited 2017-11-21 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 191–307（117 aa）
Not recorded CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；50 mM Tris-HCl at pH 8.5 containing 25% PEG-8K, 2 mM CaCl2 and 3% 1,6-diaminohexane
Resolution 1.95 Å R-free 0.202
6F1H C1rC1s complex Deposited 2017-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–308（291 aa）
Not recorded CA CALCIUM ION × 6 NA SODIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.50 Å R-free 0.340
6F1H C1rC1s complex Deposited 2017-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 18–308（291 aa）
Not recorded CA CALCIUM ION × 6 NA SODIUM ION × 3 LYS LYSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 4.50 Å R-free 0.340
6F39 C1r homodimer CUB1-EGF-CUB2 Deposited 2017-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 22–306（285 aa）
Chain B 22–306（285 aa）
Not recorded CA CALCIUM ION × 6 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；12-18% PEG 8000, 100 mM Imidazole at pH 8.0
Resolution 5.80 Å R-free 0.338
7MZT Borrelia burgdorferi BBK32-C in complex with an autolytic fragment of human C1r at 4.1A Deposited 2021-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 300–463（164 aa）
Chain B 464–705（242 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium formate, 27.5% Polyethylene glycol 3,350
Resolution 4.07 Å R-free 0.372
9EKE Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant Deposited 2024-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 308–705（398 aa）
Mutation：S654A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic (pH 7.0), 20% (w/v) PEG-3350
Resolution 3.10 Å R-free 0.278
9EKE Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant Deposited 2024-12-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 308–705（398 aa）
Mutation：S654A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate tribasic (pH 7.0), 20% (w/v) PEG-3350
Resolution 3.10 Å R-free 0.278

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

View Construct and Data Evidence
UniProt name C1R_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–398； UniProt 308–705 Author chain D； PDBConstruct 1–398； UniProt 308–705

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9ekd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ekd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ekd
Deposition date deposition_date2024-12-02
Structure title titleStructure of a C1r Zymogen Fragment Bound to SALO
Keywords keywordscomplement system, C1r, zymogen, inhibitor, IMMUNE SYSTEM, HYDROLASE; IMMUNE SYSTEM,HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.46 Å
Radius of gyration Rg (electron density) rg_electron41.70 Å
Forward intensity I(0) i0192276000.00
Molecular weight molecular_weight108890.0 kDa
Excluded volume excluded_volume134760 ų
Envelope volume envelope_volume191800 ų
Hydration-shell volume shell_volume42871 ų
Envelope diameter envelope_diameter152.4 Å
Shell Rg shell_rg41.50 Å
Envelope Rg envelope_rg42.20 Å
Shape Rg shape_rg41.67 Å
Total Rg total_rg41.78 Å
Total atoms total_atoms7644
Residues n_residues951
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax148.4 Å
Rg (real space) rg_real41.81 Å
Rg uncertainty (real space) rg_real_error1.79 Å
I(0) (real space) i0_real1.9230e+08
I(0) uncertainty (real space) i0_real_error3.4790e+06
Rg (reciprocal space) rg_reciprocal41.47 Å
I(0) (reciprocal space) i0_reciprocal192200000.0000
Solution quality estimate total_estimate0.8255
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.9 Å
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.107
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15070000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.620
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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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8. Citations (1)

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9. Files and Curves (10)