SAXSdb — 7q6c

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

Complement component C6

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 769–934	Not recorded	CP010 heavy chain × 1 kappa specific nanobody × 1 CP010 light chain × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.4；291 K；112 mM calcium acetate, 56 mM sodium cacodylate pH 6.4, 8.5% PEG8000 and 16% glycerol	Resolution 2.29 Å R-free 0.233

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 7Q6C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3T5O Crystal Structure of human Complement Component C6 Deposited 2011-07-27	Different construct 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 22–934（913 aa）	Not recorded	CD CADMIUM ION × 1 FUL beta-L-fucopyranose × 1 MAN alpha-D-mannopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；284 K；5 mM MES, 89 mM Sodium Chloride, 0.01 mM Cadmium Chloride, pH 5.8, EVAPORATION, temperature 284K	Resolution 2.87 Å R-free 0.276
4A5W Crystal structure of C5b6 Deposited 2011-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–934（913 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 FUC alpha-L-fucopyranose × 1 MAN alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；167 MM HEPES-NAOH PH7.8	Resolution 3.50 Å R-free 0.270
4E0S Crystal Structure of C5b-6 Deposited 2012-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–934（913 aa）	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 1 MAN alpha-D-mannopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；298 K；0.08M lithium chloride, 0.01M imidazole-HCl, pH 7.6, SMALL TUBES, temperature 298K	Resolution 4.21 Å R-free 0.278
6H03 OPEN CONFORMATION OF THE MEMBRANE ATTACK COMPLEX Deposited 2018-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 22–934（913 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
6H04 Closed conformation of the Membrane Attack Complex Deposited 2018-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 22–934（913 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
7NYC cryoEM structure of 3C9-sMAC Deposited 2021-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 22–934（913 aa）	Not recorded	MAN alpha-D-mannopyranose × 7 CA CALCIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FUC alpha-L-fucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
7NYD cryoEM structure of 2C9-sMAC Deposited 2021-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 22–934（913 aa）	Not recorded	MAN alpha-D-mannopyranose × 6 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FUC alpha-L-fucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
8B0F CryoEM structure of C5b8-CD59 Deposited 2022-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–934（934 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8B0G 2C9, C5b9-CD59 structure Deposited 2022-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–934（934 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8B0H 2C9, C5b9-CD59 cryoEM structure Deposited 2022-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 1–934（934 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 120 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CO6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 769–934

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	7q6c
Deposition date deposition_date	2021-11-06
Structure title title	complement C6 FIM1-2 bound to CP010 antibody
Keywords keywords	complement antibody terminal pathway, IMMUNE SYSTEM; IMMUNE SYSTEM
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	33.18 Å
Radius of gyration Rg (electron density) rg_electron	32.47 Å
Forward intensity I(0) i0	106188000.00
Molecular weight molecular_weight	78805.0 kDa
Excluded volume excluded_volume	97226 Å³
Envelope volume envelope_volume	129880 Å³
Hydration-shell volume shell_volume	34665 Å³
Envelope diameter envelope_diameter	109.1 Å
Shell Rg shell_rg	37.97 Å
Envelope Rg envelope_rg	32.33 Å
Shape Rg shape_rg	32.41 Å
Total Rg total_rg	33.07 Å
Total atoms total_atoms	10815
Residues n_residues	723
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	107.0 Å
Rg (real space) rg_real	33.26 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	1.0620e+08
I(0) uncertainty (real space) i0_real_error	1.7190e+06
Rg (reciprocal space) rg_reciprocal	33.23 Å
I(0) (reciprocal space) i0_reciprocal	106200000.0000
Solution quality estimate total_estimate	0.8949
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.625
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10730000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Complement component C6
Molecular weight formula_weight	18478.0 kDa
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	10943

LKGHCQLGQKQSGSECICMSPEEDCSHHSEDLCVFDTDSNDYFTSPACKFLAEKCLNNQQLHFLHIGSCQDGRQLEWGLERTRLSSASTKKESCGYDTCYDWEKCSASTSKCVCLLPPQCFKGGNQLYCVKMGSSTSEKTLNICEVGTIRCANRKMEILHPGKCLA

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	CP010 heavy chain
Molecular weight formula_weight	23490.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESDGGLVQPGGSLKLSCAASGFTFSDYYMAWVRQGPGKGLEWVATINYDGSSTYYRESVKGRFTISRDNAKNTLYLQMNSLRAEDTATYYCARPSTEALFAYWGHGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESS

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	kappa specific nanobody
Molecular weight formula_weight	13375.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

QVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSSE

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	CP010 light chain
Molecular weight formula_weight	23851.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DVVLTQTPSTLSVTPGQPASISCRSSQSLLNDVGNTYLYWYLQKPGQSPQLLIYLVSDLGSGVPNRFSGSGSGTDFTLKISRVEAEDVGIYYCMQASHAPYTFGQGTNLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	7q6cH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7q6cH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7q6cK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7q6cL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7q6cL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	161.057 Å
Unit-cell length b length_b	63.527 Å
Unit-cell length c length_c	128.589 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.293 Å
Low-resolution limit resolution_low	44.450 Å
R factor r_factor	0.2092
R_work r_work	0.2081
R_free r_free	0.2329

fit	/app/data/saxs_computation/q6/7q6c/7q6c.fit
pddf	/app/data/pr_computation/q6/7q6c/7q6c.pr.out
profile	/app/data/saxs_computation/q6/7q6c/7q6c.dat

complement C6 FIM1-2 bound to CP010 antibody

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

Complement component C6

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)