SAXSdb — 2k3u

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

Chemotaxis inhibitory protein

Staphylococcus aureus subsp. aureus str. Newman

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 59–149	Fragment：Chemotaxis inhibiting protein CHIPS(59-149).	C5a anaphylatoxin chemotactic receptor 1 × 1 （P21730）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CHIPS_STAAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 59–149

C5a anaphylatoxin chemotactic receptor 1

OrganismNot specified

UniProt P21730

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 B； UniProt 7–28	Fragment：C5aR(P7-28S) Non-standard monomer：Yes (specific site not provided by mmCIF)	Chemotaxis inhibitory protein × 1 （A6QIG7）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2K3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5O9H Crystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1 (C5aR) in complex with NDT9513727 Deposited 2017-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–333（303 aa） Chain B 31–333（303 aa）	Mutation：S85A, I91A, I142A, N146R, A156L, F172A, R232A, A234E, L311E, S317E, N321E Mutation：S85A, I91A, I142A, N146R, A156L, F172A, R232A, A234E, L311E, S317E, N321E	9P2 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine × 2 TLA L(+)-TARTARIC ACID × 3 OLA OLEIC ACID × 32 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；295.65 K；100mM tri-sodium citrate pH 5.5, 200mM Na/K tartrate, 35-45% (v/v) polyethylene glycol 400	Resolution 2.70 Å R-free 0.238
6C1Q Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727 Deposited 2018-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–331（302 aa） Fragment：cytochrome (UNP residues 23-127) + C5a receptor (UNP residues 30-331)	Mutation：M29W, H124I, R128L Non-standard monomer：Yes (specific site not provided by mmCIF)	9P2 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.5；283 K；25-35% PEG300, 100 mM MES, pH 6.5, 80-150 mM sodium malonate, 0.5% P400, 5 uM NDT, 5 uM PMX53	Resolution 2.90 Å R-free 0.286
6C1R Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist avacopan Deposited 2018-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–331（302 aa） Fragment：cytochrome (UNP residues 23-127) + C5a receptor (UNP residues 30-331)	Mutation：M29W, H124I, R128L Non-standard monomer：Yes (specific site not provided by mmCIF)	EFD avacopan × 1 MLI MALONATE ION × 2 NA SODIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 OLA OLEIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.5；283 K；25-32% PEG300, 100 mM MES, pH6.5, 90-120 mM sodium malonate, 1% P400, 5 uM avacopan, 5 uM PMX53	Resolution 2.20 Å R-free 0.224
7Y64 Cryo-EM structure of C5a-bound C5aR1 in complex with Gi protein Deposited 2022-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–330（330 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7Y65 Cryo-EM structure of C5a peptide-bound C5aR1 in complex with Gi protein Deposited 2022-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–330（330 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7Y66 Cryo-EM structure of BM213-bound C5aR1 in complex with Gi protein Deposited 2022-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–330（330 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7Y67 Cryo-EM structure of C089-bound C5aR1(I116A) mutant in complex with Gi protein Deposited 2022-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–330（330 aa）	Mutation：I116A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8GO8 Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 Deposited 2022-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain U 331–350（20 aa） Chain V 331–350（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 3.41 Å
8HK5 C5aR1-Gi-C5a protein complex Deposited 2022-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–350（350 aa）	Not recorded	PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I0N Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine) Deposited 2023-01-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain U 334–342（9 aa） Chain V 334–342（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 3.26 Å
8I0Z Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine) Deposited 2023-01-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 331–350（20 aa） Chain U 331–350（20 aa） Chain V 331–350（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 4.33 Å
8IA2 Structure of C5a bound human C5aR1 in complex with Go (Composite map) Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8JZP Structure of mouse C5a-human C5aR1-Go complex Deposited 2023-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
8JZZ Structure of human C5a-desArg bound human C5aR1 in complex with Go Deposited 2023-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9KUG Structure of EP67 bound to human C5aR1 in complex with Go Deposited 2024-12-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9UMR Structure of C5a-pep bound human C5aR1 in complex with Go Deposited 2025-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9UMX Structure of EP54 bound human C5aR1 in complex with Go Deposited 2025-04-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–350（349 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C5AR1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–23； UniProt 7–28

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	2k3u
Deposition date deposition_date	2008-05-16
Structure title title	Structure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.
Keywords keywords	;Chemotaxis Inhibitory Protein (CHIPS), sulfated tyrosine, GPCR membrane protein C5aR, anaphylotoxin C5a, Staphylococcus Aureus, complement cascade, Secreted, Virulence, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.65 Å
Radius of gyration Rg (electron density) rg_electron	14.32 Å
Forward intensity I(0) i0	1508220000.00
Molecular weight molecular_weight	329770.0 kDa
Excluded volume excluded_volume	412580 Å³
Envelope volume envelope_volume	47392 Å³
Hydration-shell volume shell_volume	20226 Å³
Envelope diameter envelope_diameter	68.5 Å
Shell Rg shell_rg	26.26 Å
Envelope Rg envelope_rg	20.38 Å
Shape Rg shape_rg	14.29 Å
Total Rg total_rg	14.66 Å
Total atoms total_atoms	45925
Residues n_residues	2775
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	36.6 Å
Rg (real space) rg_real	13.95 Å
Rg uncertainty (real space) rg_real_error	0.03 Å
I(0) (real space) i0_real	1.4420e+09
I(0) uncertainty (real space) i0_real_error	1.1010e+07
Rg (reciprocal space) rg_reciprocal	14.63 Å
I(0) (reciprocal space) i0_reciprocal	1508000000.0000
Solution quality estimate total_estimate	0.6853
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.030
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	2.7880
Highest regularization parameter α highest_alpha	252200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.999; Stabil: 0.974; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2k3uA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	390 — Chemotaxis-inhibiting protein CHIPS

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Chemotaxis inhibitory protein
Molecular weight formula_weight	10476.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	45925

来源生物 organism	Staphylococcus aureus subsp. aureus str. Newman
NCBI Class编号 ncbi_taxonomy_id	426430
宿主生物 host_organism	Escherichia coli

Structure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.

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

Chemotaxis inhibitory protein

State in the Current Structure

Other States of the Same Protein in the Database

C5a anaphylatoxin chemotactic receptor 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/k3/2k3u/2k3u.fit
pddf	/app/data/pr_computation/k3/2k3u/2k3u.pr.out
profile	/app/data/saxs_computation/k3/2k3u/2k3u.dat