3wwk

Crystal structure of CLEC-2 in complex with rhodocytin

Method: X-RAY DIFFRACTION

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

C-type lectin domain family 1 member B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Snaclec rhodocytin subunit alpha × 1 （Q9I841） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Snaclec rhodocytin subunit alpha × 1 （Q9I841） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Snaclec rhodocytin subunit alpha × 1 （Q9I841） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Snaclec rhodocytin subunit alpha × 1 （Q9I841） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLC1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 3–128； UniProt 96–221 Author chain F； PDBConstruct 3–128； UniProt 96–221 Author chain I； PDBConstruct 3–128； UniProt 96–221 Author chain L； PDBConstruct 3–128； UniProt 96–221

Snaclec rhodocytin subunit alpha

OrganismNot specified

UniProt Q9I841

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit beta × 1 （Q9I840）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SLYA_CALRH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain D； PDBConstruct 1–136； UniProt 1–136 Author chain G； PDBConstruct 1–136； UniProt 1–136 Author chain J； PDBConstruct 1–136； UniProt 1–136

Snaclec rhodocytin subunit beta

OrganismNot specified

UniProt Q9I840

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit alpha × 1 （Q9I841）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit alpha × 1 （Q9I841）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit alpha × 1 （Q9I841）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	C-type lectin domain family 1 member B × 1 （Q9P126） Snaclec rhodocytin subunit alpha × 1 （Q9I841）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SLYB_CALRH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–146； UniProt 1–146 Author chain E； PDBConstruct 1–146； UniProt 1–146 Author chain H； PDBConstruct 1–146； UniProt 1–146 Author chain K； PDBConstruct 1–146； UniProt 1–146

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	3wwk
Deposition date deposition_date	2014-06-20
Structure title title	Crystal structure of CLEC-2 in complex with rhodocytin
Keywords keywords	C-type lectin fold, Carbohydrate binding, Podoplanin, Rhodocytin, SUGAR BINDING PROTEIN; 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.

3wwk__assembly_1__model_1

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

Download this curve (.dat)

3wwk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wwk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.02 Å
Rg (electron density)	31.45 Å
Total Rg	31.78 Å
Atom count	3125
Residues	378
Excluded volume	54618 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wwk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wwk__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3wwk__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3wwk__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	C-type lectin domain family 1 member B
Molecular weight formula_weight	15157.0 kDa
Mutation mutation	C96S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I,L,F
Atom count atom_count	12453

GSGHKSSPCDTNWRYYGDSCYGFFRHNLTWEESKQYCTDMNATLLKIDNRNIVEYIKARTHLIRWVGLSRQKSNEVWKWEDGSVISENMFEFLEDGKGNMNCAYFHNGKMHPTFCENKHYLMCERKAG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Snaclec rhodocytin subunit alpha
Molecular weight formula_weight	15812.4 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J

GLEDCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLPY

Entity 3 Entity 3 polymer

Description description	Snaclec rhodocytin subunit beta
Molecular weight formula_weight	16790.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MGRFIFVSFGLLVVFLSLSGTGADCPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3wwka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwkb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwkc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d3wwkd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwke_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d3wwkf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d3wwkg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwkh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwki_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d3wwkj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwkk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3wwkl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3wwkA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkH00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkJ00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3wwkL00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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Unit-cell length a length_a	130.851 Å
Unit-cell length b length_b	117.072 Å
Unit-cell length c length_c	152.238 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.980 Å
Low-resolution limit resolution_low	37.560 Å
R factor r_factor	0.2841
R_work r_work	0.2819
R_free r_free	0.3249

Crystal structure of CLEC-2 in complex with rhodocytin

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

C-type lectin domain family 1 member B

State in the Current Structure

Other States of the Same Protein in the Database

Snaclec rhodocytin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Snaclec rhodocytin subunit beta

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

3wwk__assembly_1__model_1

3wwk__assembly_1__model_1 | I(q)

3wwk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of CLEC-2 in complex with rhodocytin

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

C-type lectin domain family 1 member B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Snaclec rhodocytin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Snaclec rhodocytin subunit beta

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

3wwk__assembly_1__model_1

3wwk__assembly_1__model_1 | I(q)

3wwk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)