SAXSdb — 1xd5

▼

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

antifungal protein GAFP-1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9AXZ2_9ASPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 1–112 Author chain B； PDBConstruct 1–112； UniProt 1–112 Author chain C； PDBConstruct 1–112； UniProt 1–112 Author chain D； PDBConstruct 1–112； UniProt 1–112

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xd5
Deposition date deposition_date	2004-09-04
Structure title title	Crystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata
Keywords keywords	monocot mannose binding lectin, monomer, homogeneous beta-sheet, antifungal protein; ANTIFUNGAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1xd5__assembly_1__model_1

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

Download this curve (.dat)

1xd5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xd5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.94 Å
Rg (electron density)	13.24 Å
Total Rg	14.42 Å
Atom count	876
Residues	112
Excluded volume	15083 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xd5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xd5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1xd5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1xd5__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1xd5__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1xd5a_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1xd5b_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1xd5c_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

Domain ID domain_id	d1xd5d_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.1 — alpha-D-mannose-specific plant lectins

CATH v4.4 (4 domains)

Domain ID domain_id	1xd5A00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1xd5B00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1xd5C00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	1xd5D00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

▶

Unit-cell length a length_a	61.087 Å
Unit-cell length b length_b	91.488 Å
Unit-cell length c length_c	81.132 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.690 Å
R factor r_factor	0.1674
R_work r_work	0.1655
R_free r_free	0.2061

Description description	antifungal protein GAFP-1
Molecular weight formula_weight	12307.4 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3717

Crystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata

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

antifungal protein GAFP-1

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

1xd5__assembly_1__model_1

1xd5__assembly_1__model_1 | I(q)

1xd5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

Crystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata

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

antifungal protein GAFP-1

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

1xd5__assembly_1__model_1

1xd5__assembly_1__model_1 | I(q)

1xd5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)