SAXSdb — 2fmd

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

Lectin

OrganismNot specified

UniProt P42088

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 4 其他Polymer 4	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 4 CALCIUM ION × 4 MANGANESE (II) ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEC_BOWMI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240

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	2fmd
Deposition date deposition_date	2006-01-09
Structure title title	Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin
Keywords keywords	LEGUME LECTIN, BETA SANDWICH, PROTEIN-CARBOHYDRATE COMPLEX, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fmd__assembly_1__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： An atom element in a polymer residue is ambiguous, so a reliable calculation is not possible.

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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	Lectin
Molecular weight formula_weight	25583.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1974

ANSVCFTFTDFESGQQDLIFQGDASVGSNKALQLTKVDSKGNPQGGSVGRALYTAPIRLWQSSSLVASFETTFTFSISQGSSTPADALTFFIASPDTKIPSGSGGRLLGLFGSSNNAGSDNGVVSVEFDTYPNTDIGDPNYRHIGIDVNSIRSKAASKWDWQNGKTATAHISYNSASKRLSVVSSYPNSSPVVVSFDVELNNVBPBWVRVGFSATTGQYTQTNNILAWSFRSSLMGYQAN

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

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	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	213

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2fmda_
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

CATH v4.4 (1 domains)

Domain ID domain_id	2fmdA00
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	66.603 Å
Unit-cell length b length_b	86.351 Å
Unit-cell length c length_c	91.760 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1860
R_work r_work	0.1830
R_free r_free	0.2280

Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin

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

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

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

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)

Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin

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

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

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

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)