SAXSdb — 5ubm

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

Complement C1s subcomponent

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Gigastasin × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C1S_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–252； UniProt 437–688 Author chain B； PDBConstruct 1–152； UniProt 285–436

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	5ubm
Deposition date deposition_date	2016-12-20
Structure title title	Crystal structure of human C1s in complex with inhibitor gigastasin
Keywords keywords	Complement system C1s protease inhibitor complex, IMMUNE SYSTEM-INHIBITOR complex; IMMUNE SYSTEM/INHIBITOR
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.

5ubm__assembly_1__model_1

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

Download this curve (.dat)

5ubm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ubm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.70 Å
Rg (electron density)	33.99 Å
Total Rg	34.05 Å
Atom count	3810
Residues	493
Excluded volume	67125 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ubm__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Complement C1s subcomponent
Molecular weight formula_weight	27841.7 kDa
EC 编号 ec_number	3.4.21.42
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3936

RIIGGSDADIKNFPWQVFFDNPWAGGALINEYWVLTAAHVVEGNREPTMYVGSTSVQTSRLAKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIALVRLKDPVKMGPTVSPICLPGTSSDYNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAPLRKCKEVKVEKPTADAEAYVFTPNMICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAGLVSWGPQCGTYGLYTRVKNYVDWIMKTMQENSTPRED

Entity 2 Entity 2 polymer

Description description	Complement C1s subcomponent
Molecular weight formula_weight	16882.9 kDa
EC 编号 ec_number	3.4.21.42
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LRYHGDPMPCPKEDTPNSVWEPAKAKYVFRDVVQITCLDGFEVVEGRVGATSFYSTCQSNGKWSNSKLKCQPVDCGIPESIENGKVEDPESTLFGSVIRYTCEEPYYYMENGGGGEYHCAGNGSWVNEVLGPELPKCVPVCGVPREPFEEKQ

Entity 3 Entity 3 polymer

Description description	Gigastasin
Molecular weight formula_weight	16104.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

AHHHHHHTSGDDDDKAKKKLPKCQKQEDCGSWDLKCNNVTKKCECRNQVCGRGCPKERYQRDKYGCRKCLCKGCDGFKCRLGCTYGFKTDKKGCEAFCTCNTKETACVNIWCTDPYKCNPESGRCEDPNEEYEYDYE

Source Source

Source organism organism	Haementeria ghilianii
NCBI taxonomy ID ncbi_taxonomy_id	6409
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ubmb1
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d5ubmb2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5ubmA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	5ubmA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	5ubmB01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	5ubmB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

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Unit-cell length a length_a	89.350 Å
Unit-cell length b length_b	89.350 Å
Unit-cell length c length_c	146.871 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	41.372 Å
R factor r_factor	0.1790
R_work r_work	0.1767
R_free r_free	0.2223

Crystal structure of human C1s in complex with inhibitor gigastasin

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

Complement C1s subcomponent

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

5ubm__assembly_1__model_1

5ubm__assembly_1__model_1 | I(q)

5ubm__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human C1s in complex with inhibitor gigastasin

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

Complement C1s subcomponent

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

5ubm__assembly_1__model_1

5ubm__assembly_1__model_1 | I(q)

5ubm__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)