SAXSdb — 3dem

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

Complement factor MASP-3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96RS4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 20–297 Author chain B； PDBConstruct 1–278； UniProt 20–297

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	3dem
Deposition date deposition_date	2008-06-10
Structure title title	CUB1-EGF-CUB2 domain of HUMAN MASP-1/3
Keywords keywords	;complement system, innate immunity, calcium binding sites, Complement pathway, EGF-like domain, Glycoprotein, Hydrolase, Hydroxylation, Immune response, Protease, Serine protease, Sushi, Lectin ;; HYDROLASE
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.

3dem__assembly_1__model_1

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

Download this curve (.dat)

3dem__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dem__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.18 Å
Rg (electron density)	38.12 Å
Total Rg	38.09 Å
Atom count	4309
Residues	532
Excluded volume	75818 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dem__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Complement factor MASP-3
Molecular weight formula_weight	32002.3 kDa
EC 编号 ec_number	3.4.21.-
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	4650

HTVELNNMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTDTEQTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKEREDEELSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	341

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3dema1
Class class	b — All beta proteins
Fold Fold fold	b.23 — CUB-like
Superfamily Superfamily superfamily	b.23.1 — Spermadhesin, CUB domain
Family Family family	b.23.1.0 — automated matches

Domain ID domain_id	d3dema2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d3dema3
Class class	b — All beta proteins
Fold Fold fold	b.23 — CUB-like
Superfamily Superfamily superfamily	b.23.1 — Spermadhesin, CUB domain
Family Family family	b.23.1.0 — automated matches

Domain ID domain_id	d3demb1
Class class	b — All beta proteins
Fold Fold fold	b.23 — CUB-like
Superfamily Superfamily superfamily	b.23.1 — Spermadhesin, CUB domain
Family Family family	b.23.1.0 — automated matches

Domain ID domain_id	d3demb2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d3demb3
Class class	b — All beta proteins
Fold Fold fold	b.23 — CUB-like
Superfamily Superfamily superfamily	b.23.1 — Spermadhesin, CUB domain
Family Family family	b.23.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3demA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

Domain ID domain_id	3demA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	3demA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

Domain ID domain_id	3demB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

Domain ID domain_id	3demB02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	3demB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	290 — Spermadhesin, CUB domain

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Unit-cell length a length_a	88.692 Å
Unit-cell length b length_b	110.232 Å
Unit-cell length c length_c	190.587 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	16

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2230
R_work r_work	0.2220
R_free r_free	0.2450

CUB1-EGF-CUB2 domain of HUMAN MASP-1/3

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

Complement factor MASP-3

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

3dem__assembly_1__model_1

3dem__assembly_1__model_1 | I(q)

3dem__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CUB1-EGF-CUB2 domain of HUMAN MASP-1/3

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

Complement factor MASP-3

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

3dem__assembly_1__model_1

3dem__assembly_1__model_1 | I(q)

3dem__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)