SAXSdb — 4p39

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

Complement C5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–77； UniProt 678–747 Author chain B； PDBConstruct 8–77； UniProt 678–747 Author chain C； PDBConstruct 8–77； UniProt 678–747 Author chain D； PDBConstruct 8–77； UniProt 678–747

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	4p39
Deposition date deposition_date	2014-03-06
Structure title title	Crystal structure of the human C5aR antagonist C5a-A8
Keywords keywords	complement anaphylatoxin, C5a, three-helix bundle, GPCR antagonist, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

4p39__assembly_1__model_1

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

Download this curve (.dat)

4p39__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p39__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.80 Å
Rg (electron density)	16.02 Å
Total Rg	16.69 Å
Atom count	536
Residues	69
Excluded volume	9574 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p39__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4p39__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4p39__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4p39__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4p39__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4p39__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4p39__assembly_7__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 (2)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4p39a1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p39a2
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	d4p39b1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p39b2
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	d4p39c_
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p39d_
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

CATH v4.4 (4 domains)

Domain ID domain_id	4p39A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p39B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p39C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p39D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

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Unit-cell length a length_a	69.350 Å
Unit-cell length b length_b	83.240 Å
Unit-cell length c length_c	119.220 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.401 Å
Low-resolution limit resolution_low	48.644 Å
R factor r_factor	0.2247
R_work r_work	0.2236
R_free r_free	0.2377

Description description	Complement C5
Molecular weight formula_weight	8365.7 kDa
Mutation mutation	C704R
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2165

Crystal structure of the human C5aR antagonist C5a-A8

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

Complement C5

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

4p39__assembly_1__model_1

4p39__assembly_1__model_1 | I(q)

4p39__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

Crystal structure of the human C5aR antagonist C5a-A8

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

Complement C5

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

4p39__assembly_1__model_1

4p39__assembly_1__model_1 | I(q)

4p39__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)