SAXSdb — 1md7

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

C1R COMPLEMENT SERINE PROTEASE

Homo sapiens

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 375–702	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

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 1MD7	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 ligand/ion 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 ligand/ion 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 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
1MD8 Monomeric structure of the active catalytic domain of complement protease C1r Deposited 2002-08-07	Different construct Different mutation/modification Different ligand/ion 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 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 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
9EKD Structure of a C1r Zymogen Fragment Bound to SALO Deposited 2024-12-02	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 C 308–705（398 aa） Fragment：residues 308-705	Mutation：S654A	No recorded non-water small molecule	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
9EKD Structure of a C1r Zymogen Fragment Bound to SALO Deposited 2024-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 308–705（398 aa） Fragment：residues 308-705	Mutation：S654A	No recorded non-water small molecule	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
9EKE Structure of a C1r Zymogen Fragment Bound to SALO, Y51F Mutant Deposited 2024-12-02	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 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 mutation/modification Different oligomeric state Different ligand/ion 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 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C1R_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 375–702

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	1md7
Deposition date deposition_date	2002-08-07
Structure title title	Monomeric structure of the zymogen of complement protease C1r
Keywords keywords	complement, innate immunity, serine protease, activation, substrate specificity, 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	23.36 Å
Radius of gyration Rg (electron density) rg_electron	22.56 Å
Forward intensity I(0) i0	21209100.00
Molecular weight molecular_weight	34295.0 kDa
Excluded volume excluded_volume	42594 Å³
Envelope volume envelope_volume	53138 Å³
Hydration-shell volume shell_volume	21173 Å³
Envelope diameter envelope_diameter	81.5 Å
Shell Rg shell_rg	27.57 Å
Envelope Rg envelope_rg	22.84 Å
Shape Rg shape_rg	22.52 Å
Total Rg total_rg	23.32 Å
Total atoms total_atoms	2414
Residues n_residues	304
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	81.2 Å
Rg (real space) rg_real	23.51 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	2.1210e+07
I(0) uncertainty (real space) i0_real_error	3.0700e+05
Rg (reciprocal space) rg_reciprocal	23.47 Å
I(0) (reciprocal space) i0_reciprocal	21210000.0000
Solution quality estimate total_estimate	0.8417
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.0 Å
Skewness Skewness skewness	0.563
Kurtosis Kurtosis kurtosis	-0.105
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4791000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.960

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	C1R COMPLEMENT SERINE PROTEASE
Molecular weight formula_weight	37053.9 kDa
EC 编号 ec_number	3.4.21.41
Mutation mutation	S637A
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	2531

DCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQRIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDAGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEME

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1md7a1
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1md7a2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

CATH v4.4 (3 domains)

Domain ID domain_id	1md7A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	1md7A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1md7A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	167.060 Å
Unit-cell length b length_b	167.060 Å
Unit-cell length c length_c	43.648 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	11.940 Å
R factor r_factor	0.2428
R_work r_work	0.2170
R_free r_free	0.2850

fit	/app/data/saxs_computation/md/1md7/1md7.fit
pddf	/app/data/pr_computation/md/1md7/1md7.pr.out
profile	/app/data/saxs_computation/md/1md7/1md7.dat

Monomeric structure of the zymogen of complement protease C1r

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

C1R COMPLEMENT SERINE PROTEASE

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