SAXSdb — 3d5r

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

Complement C3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Fibrinogen-binding protein × 1 （A6QG59） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Fibrinogen-binding protein × 1 （A6QG59） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–297； UniProt 996–1287 Author chain B； PDBConstruct 6–297； UniProt 996–1287

Fibrinogen-binding protein

Staphylococcus aureus subsp. aureus str. Newman

UniProt A6QG59

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Complement C3 × 1 （P01024） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Complement C3 × 1 （P01024） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIB_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–65； UniProt 101–165 Author chain D； PDBConstruct 1–65； UniProt 101–165

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	3d5r
Deposition date deposition_date	2008-05-16
Structure title title	Crystal Structure of Efb-C (N138A) / C3d Complex
Keywords keywords	;Protein-protein complex, cell adhesion-toxin complex, site-directed mutation, Age-related macular degeneration, Cleavage on pair of basic residues, Complement alternate pathway, Complement pathway, Disease mutation, Glycoprotein, Immune response, Inflammatory response, Innate immunity, Phosphoprotein, Polymorphism, Secreted, Thioester bond ;; CELL ADHESION/TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3d5r__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d5r__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d5r__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.03 Å
Rg (electron density)	19.88 Å
Total Rg	20.86 Å
Atom count	2859
Residues	362
Excluded volume	51346 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d5r__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d5r__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Complement C3
Molecular weight formula_weight	33143.9 kDa
Mutation mutation	C1010A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5868

GSRSTDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Fibrinogen-binding protein
Molecular weight formula_weight	7549.9 kDa
Mutation mutation	N138A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

TDATIKKEQKLIQAQNLVREFEKTHTVSAHRKAQKAVALVSFEYKVKKMVLQERIDNVLKQGLVR

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus str. Newman
NCBI taxonomy ID ncbi_taxonomy_id	426430
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3d5ra2
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.4 — Complement components

Domain ID domain_id	d3d5ra3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d5rb2
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.4 — Complement components

Domain ID domain_id	d3d5rb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3d5rc1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.17 — Efb C-domain-like
Family Family family	a.7.17.1 — Efb C-domain-like

Domain ID domain_id	d3d5rd_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.17 — Efb C-domain-like
Family Family family	a.7.17.1 — Efb C-domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	3d5rA00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3d5rB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3d5rC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1270 — Sbi, C3 binding domain IV

Domain ID domain_id	3d5rD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1270 — Sbi, C3 binding domain IV

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Unit-cell length a length_a	91.010 Å
Unit-cell length b length_b	91.010 Å
Unit-cell length c length_c	120.520 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2180
R_free r_free	0.2410

Crystal Structure of Efb-C (N138A) / C3d Complex

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

Complement C3

State in the Current Structure

Other States of the Same Protein in the Database

Fibrinogen-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d5r__assembly_2__model_1

3d5r__assembly_2__model_1 | I(q)

3d5r__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Efb-C (N138A) / C3d Complex

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

Complement C3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fibrinogen-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d5r__assembly_2__model_1

3d5r__assembly_2__model_1 | I(q)

3d5r__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)