4r9j

L-ficolin complexed to glucosamine-6-sulfate

Method: X-RAY DIFFRACTION

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

Ficolin-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 1	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 ACETATE ION × 7 SULFATE ION × 1 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 ACETATE ION × 2 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 ACETATE ION × 2 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose × 2 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 ACETATE ION × 3 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FCN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 97–313 Author chain B； PDBConstruct 1–217； UniProt 97–313 Author chain G； PDBConstruct 1–217； UniProt 97–313

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	4r9j
Deposition date deposition_date	2014-09-05
Structure title title	L-ficolin complexed to glucosamine-6-sulfate
Keywords keywords	;FIBRINOGEN-LIKE domain, INNATE IMMUNITY, PATTERN RECOGNITION PROTEIN, LECTIN, IMMUNOLOGY, LECTIN-LIKE, SUGAR BINDING PROTEIN, plasma, extracellular ;; SUGAR BINDING PROTEIN
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.

4r9j__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4r9j__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r9j__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	17.85 Å
Rg (electron density)	16.73 Å
Total Rg	17.84 Å
Atom count	1792
Residues	217
Excluded volume	31282 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r9j__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4r9j__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4r9j__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4r9j__assembly_4__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Ficolin-2
Molecular weight formula_weight	24611.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,A,B
Atom count atom_count	5653

PCLTGPRTCKDLLDRGHFLSGWHTIYLPDCRPLTVLCDMDTDGGGWTVFQRRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRVDLVDFEDNYQFAKYRSFKVADEAEKYNLVLGAFVEGSAGDSLTFHNNQSFSTKDQDNDLNTGNCAVMFQGAWWYKNCHVSNLNGRYLRGTHGSFANGINWKSGKGYNYSYKVSEMKVRPA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Unidentified Baculovirus

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 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	4

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
Molecular weight formula_weight	259.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 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 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4r9ja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d4r9jb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

Domain ID domain_id	d4r9jg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.171 — Fibrinogen C-terminal domain-like
Superfamily Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
Family Family family	d.171.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4r9jA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	4r9jA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	4r9jB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	4r9jB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	4r9jG01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	4r9jG02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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Unit-cell length a length_a	97.170 Å
Unit-cell length b length_b	97.170 Å
Unit-cell length c length_c	139.990 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.1739
R_work r_work	0.1724
R_free r_free	0.2034

L-ficolin complexed to glucosamine-6-sulfate

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

Ficolin-2

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

4r9j__assembly_4__model_1

4r9j__assembly_4__model_1 | I(q)

4r9j__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

L-ficolin complexed to glucosamine-6-sulfate

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

Ficolin-2

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

4r9j__assembly_4__model_1

4r9j__assembly_4__model_1 | I(q)

4r9j__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)