SAXSdb — 2cm4

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

COMPLEMENT INHIBITOR

ORNITHODOROS MOUBATA

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 19–168	Mutation：YES	ACT ACETATE ION × 1 RCL RICINOLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；30% PEG 4000 0.1 M SODIUM ACETATE PH 4.6 0.2 M AMMONIUM ACETATE	Resolution 1.90 Å

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 2CM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CM9 The complement inhibitor OmCI in complex with ricinoleic acid Deposited 2006-05-04	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–168（150 aa）	Mutation：YES	RCL RICINOLEIC ACID × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30% PEG 4000 0.1 M SODIUM ACETATE PH 4.6 0.2 M AMMONIUM ACETATE	Resolution 2.30 Å
3ZUI OMCI in complex with palmitoleic acid Deposited 2011-07-19	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 19–168（150 aa）	Not recorded	PAM PALMITOLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS PH 8.5.	Resolution 1.71 Å R-free 0.223
3ZUO OMCI in complex with leukotriene B4 Deposited 2011-07-19	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 19–168（150 aa）	Not recorded	LTB LEUKOTRIENE B4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4.	Resolution 1.86 Å R-free 0.238
3ZUO OMCI in complex with leukotriene B4 Deposited 2011-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–168（150 aa）	Not recorded	LTB LEUKOTRIENE B4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4.	Resolution 1.86 Å R-free 0.238
3ZUO OMCI in complex with leukotriene B4 Deposited 2011-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 19–168（150 aa）	Not recorded	LTB LEUKOTRIENE B4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4.	Resolution 1.86 Å R-free 0.238
3ZUO OMCI in complex with leukotriene B4 Deposited 2011-07-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 19–168（150 aa）	Not recorded	LTB LEUKOTRIENE B4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.4；21% PEG 4000, 0.2 M SODIUM ACETATE, TRIS 0.1 M PH 8.4.	Resolution 1.86 Å R-free 0.238
5HCC Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Dermacentor andersoni RaCI3. Deposited 2016-01-04	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 C 19–168（150 aa）	Mutation：N78Q, N102Q	EDO 1,2-ETHANEDIOL × 7 CYS CYSTEINE × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；10% PEG 20K, 2% v/v 1,4 Dioxane, 0.1 M Bicine pH 9.0	Resolution 2.59 Å R-free 0.267
5HCD Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Rhipicephalus microplus RaCI2 Deposited 2016-01-04	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 C 19–168（150 aa） Fragment：UNP residues 19-168	Mutation：N78Q, N102Q	CYS CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；10% (w/v) PEG 20K, 2%(v/v)1,4 Dioxane, 0.1M Bicine pH 9.0	Resolution 2.98 Å R-free 0.282
5HCE Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Rhipicephalus appendiculatus RaCI1 Deposited 2016-01-04	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 C 19–168（150 aa） Fragment：UNP residues 19-168	Mutation：N78Q, N102Q	CYS CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；10% PEG 6K, 0.1 M Bicine pH 9.0	Resolution 3.12 Å R-free 0.281
6RQJ Structure of human complement C5 complexed with tick inhibitors OmCI, RaCI1 and CirpT1 Deposited 2019-05-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 19–168（150 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	Q5YD59_ORNMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 19–168

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	2cm4
Deposition date deposition_date	2006-05-04
Structure title title	The complement inhibitor OmCI in complex with ricinoleic acid
Keywords keywords	ORNITHODOROS MOUBATA, C5, TICK, OMCI, LIPOCALIN, INHIBITOR, COMPLEMENT; INHIBITOR
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	15.72 Å
Radius of gyration Rg (electron density) rg_electron	14.32 Å
Forward intensity I(0) i0	5821750.00
Molecular weight molecular_weight	16627.0 kDa
Excluded volume excluded_volume	20494 Å³
Envelope volume envelope_volume	23247 Å³
Hydration-shell volume shell_volume	13526 Å³
Envelope diameter envelope_diameter	48.0 Å
Shell Rg shell_rg	20.34 Å
Envelope Rg envelope_rg	14.71 Å
Shape Rg shape_rg	14.30 Å
Total Rg total_rg	15.54 Å
Total atoms total_atoms	1162
Residues n_residues	145
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	48.1 Å
Rg (real space) rg_real	15.60 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	5.8220e+06
I(0) uncertainty (real space) i0_real_error	6.0830e+04
Rg (reciprocal space) rg_reciprocal	15.61 Å
I(0) (reciprocal space) i0_reciprocal	5822000.0000
Solution quality estimate total_estimate	0.7279
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1221000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.987; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	COMPLEMENT INHIBITOR
Molecular weight formula_weight	16832.6 kDa
Mutation mutation	YES
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	1329

DSESDCTGSEPVDAFQAFSEGKEAYVLVRSTDPKARDCLKGEPAGEKQDNTLPVMMTFKQGTDWASTDWTFTLDGAKVTATLGQLTQNREVVYDSQSHHCHVDKVEKEVPDYEMWMLDAGGLEVEVECCRQKLEELASGRNQMYPHLKDC

来源 Source

来源生物 organism	ORNITHODOROS MOUBATA
通用名 common_name	SOFT TICK
NCBI Class编号 ncbi_taxonomy_id	6938
宿主生物 host_organism	PICHIA METHANOLICA

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	RICINOLEIC ACID
Molecular weight formula_weight	298.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2cm4A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	45.170 Å
Unit-cell length b length_b	55.520 Å
Unit-cell length c length_c	60.620 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	40.900 Å
R factor r_factor	0.1690
R_work r_work	0.1690
R_free r_free	—

fit	/app/data/saxs_computation/cm/2cm4/2cm4.fit
pddf	/app/data/pr_computation/cm/2cm4/2cm4.pr.out
profile	/app/data/saxs_computation/cm/2cm4/2cm4.dat

The complement inhibitor OmCI in complex with ricinoleic acid

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

COMPLEMENT INHIBITOR

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