SAXSdb — 3lm1

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

Agglutinin alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Agglutinin beta-2 chain × 4 （P18676） 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Agglutinin beta-2 chain × 4 （P18676） 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 3 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LECA_MACPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 1–133 Author chain C； PDBConstruct 1–133； UniProt 1–133 Author chain E； PDBConstruct 1–133； UniProt 1–133 Author chain G； PDBConstruct 1–133； UniProt 1–133 Author chain I； PDBConstruct 1–133； UniProt 1–133 Author chain K； PDBConstruct 1–133； UniProt 1–133 Author chain M； PDBConstruct 1–133； UniProt 1–133 Author chain O； PDBConstruct 1–133； UniProt 1–133

Agglutinin beta-2 chain

OrganismNot specified

UniProt P18676

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Agglutinin alpha chain × 4 （P18674） 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Agglutinin alpha chain × 4 （P18674） 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 3 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LECB2_MACPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； UniProt 2–16 Author chain D； PDBConstruct 1–15； UniProt 2–16 Author chain F； PDBConstruct 1–15； UniProt 2–16 Author chain H； PDBConstruct 1–15； UniProt 2–16 Author chain J； PDBConstruct 1–15； UniProt 2–16 Author chain L； PDBConstruct 1–15； UniProt 2–16 Author chain N； PDBConstruct 1–15； UniProt 2–16 Author chain P； PDBConstruct 1–15； UniProt 2–16

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	3lm1
Deposition date deposition_date	2010-01-29
Structure title title	Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc
Keywords keywords	Maclura pomifera agglutinin, MPA, MPA complex, (p)-nitrophenyl-GalNAc, Lectin, 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.

3lm1__assembly_1__model_1

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

Download this curve (.dat)

3lm1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lm1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.82 Å
Rg (electron density)	26.83 Å
Total Rg	27.52 Å
Atom count	4733
Residues	591
Excluded volume	84625 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lm1__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lm1__assembly_2__model_1`	octameric （8）	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	Agglutinin alpha chain
Molecular weight formula_weight	14768.6 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	10310

GVTFDDGAYTGIREINFEYNSETAIGGLRVTYDLNGMPFVAEDHKSFITGFKPVKISLEFPSEYIVEVSGYVGKVEGYTVIRSLTFKTNKQTYGPYGVTNGTPFSLPIENGLIVGFKGSIGYWLDYFSIYLSL

Entity 2 Entity 2 polymer

Description description	Agglutinin beta-2 chain
Molecular weight formula_weight	1615.8 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

RNGKSQSIIVGPWGD

Entity 3 Entity 3 non-polymer

Description description	4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside
Molecular weight formula_weight	342.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	879

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3lm1A00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1C00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1E00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1G00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1I00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1K00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1M00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	3lm1O00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

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Unit-cell length a length_a	69.090 Å
Unit-cell length b length_b	133.290 Å
Unit-cell length c length_c	200.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2440

Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc

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

Agglutinin alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Agglutinin beta-2 chain

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

3lm1__assembly_1__model_1

3lm1__assembly_1__model_1 | I(q)

3lm1__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc

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

Agglutinin alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Agglutinin beta-2 chain

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

3lm1__assembly_1__model_1

3lm1__assembly_1__model_1 | I(q)

3lm1__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)