3m3e

Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with p-Nitrophenyl Thomsen-Friedenreich disaccharide

Method: X-RAY DIFFRACTION

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

Anti-tumor lectin

Agrocybe aegerita

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 P-NITROPHENOL × 2 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 2	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 P-NITROPHENOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATLE_AGRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–159； UniProt 1–158 Author chain B； PDBConstruct 2–159； UniProt 1–158 Author chain C； PDBConstruct 2–159； UniProt 1–158 Author chain D； PDBConstruct 2–159； UniProt 1–158

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	3m3e
Deposition date deposition_date	2010-03-09
Structure title title	Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with p-Nitrophenyl Thomsen-Friedenreich disaccharide
Keywords keywords	;galectin, AAL, mutant, Thomsen-Friedenreich disaccharide, Apoptosis, Hydrolase, Lectin, Nuclease, GAL-BETA-1, 3-GALNAC-ALPHA-O-p-Nitrophenyl ;; 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.

3m3e__assembly_1__model_1

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

Download this curve (.dat)

3m3e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m3e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.64 Å
Rg (electron density)	20.42 Å
Total Rg	21.20 Å
Atom count	2474
Residues	318
Excluded volume	43884 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m3e__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3m3e__assembly_2__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	Anti-tumor lectin
Molecular weight formula_weight	17293.2 kDa
EC 编号 ec_number	3.1.21.-
Mutation mutation	E66A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5556

MQGVNIYNISAGTSVDLAAPVTTGDIVTFFSSALNLNAGAGNPNNTTLNLFAENGAYLLHIAFRLQANVIIFNSRQPDGPWLVEQRVSDVANQFAGIDGKAMVTVFDHGDKYQVVINEKTVIQYTKQISGLTSSLSYNATEETSIFSTVVEAVTYTGLALE

Source Source

Source organism organism	Agrocybe aegerita
Common name common_name	Black poplar mushroom
NCBI taxonomy ID ncbi_taxonomy_id	5400
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	383.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	P-NITROPHENOL
Molecular weight formula_weight	139.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	582

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3m3ea1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3m3ea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3m3eb1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3m3eb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3m3ec1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3m3ec2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3m3ec3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3m3ed1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3m3ed2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3m3ed3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3m3eA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3m3eB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3m3eC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3m3eD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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Unit-cell length a length_a	56.820 Å
Unit-cell length b length_b	53.240 Å
Unit-cell length c length_c	103.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2060
R_free r_free	0.2570

Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with p-Nitrophenyl Thomsen-Friedenreich disaccharide

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

Anti-tumor 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

3m3e__assembly_1__model_1

3m3e__assembly_1__model_1 | I(q)

3m3e__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with p-Nitrophenyl Thomsen-Friedenreich disaccharide

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

Anti-tumor 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

3m3e__assembly_1__model_1

3m3e__assembly_1__model_1 | I(q)

3m3e__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)