4c16

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist

Method: X-RAY DIFFRACTION

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

E-SELECTIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CALCIUM ION × 1 (S)-CYCLOHEXYL LACTIC ACID × 1 beta-D-galactopyranose × 1 (1R,2R,3S)-3-methylcyclohexane-1,2-diol × 1 alpha-L-fucopyranose × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CALCIUM ION × 1 (S)-CYCLOHEXYL LACTIC ACID × 1 beta-D-galactopyranose × 1 (1R,2R,3S)-3-methylcyclohexane-1,2-diol × 1 alpha-L-fucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYAM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–280； UniProt 22–301 Author chain B； PDBConstruct 1–280； UniProt 22–301

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	4c16
Deposition date deposition_date	2013-08-09
Structure title title	E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist
Keywords keywords	CELL ADHESION, CELL-ADHESION MOLECULE, C-TYPE LECTIN, INFLAMMATION, LEUKOCYTE, GLYCOMIMETIC, ANTAGONIST, CATCH- BOND; CELL ADHESION
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.

4c16__assembly_1__model_1

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

Download this curve (.dat)

4c16__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4c16__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.22 Å
Rg (electron density)	41.17 Å
Total Rg	40.62 Å
Atom count	2319
Residues	280
Excluded volume	40715 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4c16__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4c16__assembly_2__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	E-SELECTIN
Molecular weight formula_weight	31305.8 kDa
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	5379

WSYNTSTEAMTYDEASAYCQQRYTHLVAIQNKEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNNRQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTAACTNTSCSGHGECVETINNYTCKCDPGFSGLKCEQIVNCTALESPEHGSLVCSHPLGNFSYNSSCSISCDRGYLPSSMETMQCMSSGEWSAPIPACNVVECDAVTNPANGFVECFQNPGSFPWNTTCTFDCEEGFELMGAQSLQCTSSGNWDNEKPTCKA

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	CRICETULUS GRISEUS

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	14

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	2

Entity 4 Entity 4 non-polymer

Description description	(S)-CYCLOHEXYL LACTIC ACID
Molecular weight formula_weight	172.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	(1R,2R,3S)-3-methylcyclohexane-1,2-diol
Molecular weight formula_weight	130.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	525

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4c16A01
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	4c16A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4c16A03
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	4c16A04
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	4c16B01
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	4c16B02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4c16B03
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	4c16B04
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	52.582 Å
Unit-cell length b length_b	56.917 Å
Unit-cell length c length_c	59.684 Å
Unit-cell angle α angle_alpha	74.40 °
Unit-cell angle β angle_beta	87.11 °
Unit-cell angle γ angle_gamma	88.26 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	15.810 Å
R factor r_factor	0.1830
R_work r_work	0.1803
R_free r_free	0.2324

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist

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

E-SELECTIN

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

4c16__assembly_1__model_1

4c16__assembly_1__model_1 | I(q)

4c16__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 (8)

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 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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist

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

E-SELECTIN

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

4c16__assembly_1__model_1

4c16__assembly_1__model_1 | I(q)

4c16__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 (8)

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 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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)