4yw7

Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA

Method: X-RAY DIFFRACTION

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

PA-I galactophilic lectin

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
16	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 ;(2R,3R,4S,5R,6R,2'R,3'R,4'S,5'R,6'R)-2,2'-([(2R,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]bis{1H-1,2,3-triazole-1,4-diyl[(2S,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]-1H-1,2,3-triazole-1,4-diylpropane-3,1-diyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol] ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 beta-D-galactopyranose × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 ;(2R,3R,4S,5R,6R,2'R,3'R,4'S,5'R,6'R)-2,2'-([(2R,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]bis{1H-1,2,3-triazole-1,4-diyl[(2S,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]-1H-1,2,3-triazole-1,4-diylpropane-3,1-diyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol] ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA1L_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 2–122 Author chain B； PDBConstruct 1–121； UniProt 2–122 Author chain C； PDBConstruct 1–121； UniProt 2–122 Author chain D； PDBConstruct 1–121； UniProt 2–122 Author chain E； PDBConstruct 1–121； UniProt 2–122 Author chain F； PDBConstruct 1–121； UniProt 2–122 Author chain G； PDBConstruct 1–121； UniProt 2–122 Author chain H； PDBConstruct 1–121； UniProt 2–122 Author chain I； PDBConstruct 1–121； UniProt 2–122 Author chain J； PDBConstruct 1–121； UniProt 2–122 Author chain K； PDBConstruct 1–121； UniProt 2–122 Author chain L； PDBConstruct 1–121； UniProt 2–122 Author chain M； PDBConstruct 1–121； UniProt 2–122 Author chain N； PDBConstruct 1–121； UniProt 2–122 Author chain O； PDBConstruct 1–121； UniProt 2–122 Author chain P； PDBConstruct 1–121； UniProt 2–122

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	4yw7
Deposition date deposition_date	2015-03-20
Structure title title	Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA
Keywords keywords	Galactosides, lectins, 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.

4yw7__assembly_14__model_1

Assembly 14 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4yw7__assembly_14__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yw7__assembly_14__model_1 | P(r) · Pending

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

Rg（Guinier）	15.02 Å
Rg (electron density)	13.79 Å
Total Rg	14.92 Å
Atom count	896
Residues	119
Excluded volume	15796 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yw7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4yw7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4yw7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4yw7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4yw7__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4yw7__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4yw7__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4yw7__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4yw7__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4yw7__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4yw7__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4yw7__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`4yw7__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`4yw7__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`4yw7__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`4yw7__assembly_16__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 (5)

Entity 1 Entity 1 polymer

Description description	PA-I galactophilic lectin
Molecular weight formula_weight	12770.1 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	16634

AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	;(2R,3R,4S,5R,6R,2'R,3'R,4'S,5'R,6'R)-2,2'-([(2R,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]bis{1H-1,2,3-triazole-1,4-diyl[(2S,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]-1H-1,2,3-triazole-1,4-diylpropane-3,1-diyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol] ;
Molecular weight formula_weight	1149.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1873

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d4yw7a_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7b_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7c_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7d_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7e_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7f_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7g_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7h_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7i_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7j_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7k_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7l_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7m_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7n_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7o_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

Domain ID domain_id	d4yw7p_
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.16 — PA-IL, galactose-binding lectin 1

CATH v4.4 (16 domains)

Domain ID domain_id	4yw7A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7M00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7N00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7O00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

Domain ID domain_id	4yw7P00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	430 — Galactose-binding lectin

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Unit-cell length a length_a	49.570 Å
Unit-cell length b length_b	89.310 Å
Unit-cell length c length_c	100.010 Å
Unit-cell angle α angle_alpha	90.04 °
Unit-cell angle β angle_beta	89.83 °
Unit-cell angle γ angle_gamma	79.61 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	16.034 Å
R factor r_factor	0.1809
R_work r_work	0.1789
R_free r_free	0.2206

Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA

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

PA-I galactophilic lectin

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

4yw7__assembly_14__model_1

4yw7__assembly_14__model_1 | I(q)

4yw7__assembly_14__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA

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

PA-I galactophilic lectin

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

4yw7__assembly_14__model_1

4yw7__assembly_14__model_1 | I(q)

4yw7__assembly_14__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)