SAXSdb — 4xre

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

Antifungal protein ginkbilobin-2

Ginkgo biloba

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	alpha-D-mannopyranose × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	alpha-D-mannopyranose × 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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNK2_GINBI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–109； UniProt 27–134 Author chain B； PDBConstruct 2–109； UniProt 27–134 Author chain C； PDBConstruct 2–109； UniProt 27–134 Author chain D； PDBConstruct 2–109； UniProt 27–134

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	4xre
Deposition date deposition_date	2015-01-21
Structure title title	Crystal structure of Gnk2 complexed with mannose
Keywords keywords	C-X8-C-X2-C MOTIF, ANTIFUNGAL ACTIVITY, LECTIN, ANTIFUNGAL PROTEIN; ANTIFUNGAL 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.

4xre__assembly_1__model_1

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

Download this curve (.dat)

4xre__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xre__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.19 Å
Rg (electron density)	13.00 Å
Total Rg	14.08 Å
Atom count	827
Residues	108
Excluded volume	14472 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xre__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4xre__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4xre__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4xre__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	Antifungal protein ginkbilobin-2
Molecular weight formula_weight	11802.3 kDa
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	3434

MANTAFVSSACNTQKIPSGSPFNRNLRAMLADLRQNTAFSGYDYKTSRAGSGGAPTAYGRATCKQSISQSDCTACLSNLVNRIFSICNNAIGARVQLVDCFIQYEQRSF

Source Source

Source organism organism	Ginkgo biloba
Common name common_name	maidenhair tree
NCBI taxonomy ID ncbi_taxonomy_id	3311
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	150

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4xreA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	430 — Killer Toxin P4; Chain A
Homologous superfamily homologous superfamily	20 — Gnk2 domain, C-X8-C-X2-C motif

Domain ID domain_id	4xreB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	430 — Killer Toxin P4; Chain A
Homologous superfamily homologous superfamily	20 — Gnk2 domain, C-X8-C-X2-C motif

Domain ID domain_id	4xreC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	430 — Killer Toxin P4; Chain A
Homologous superfamily homologous superfamily	20 — Gnk2 domain, C-X8-C-X2-C motif

Domain ID domain_id	4xreD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	430 — Killer Toxin P4; Chain A
Homologous superfamily homologous superfamily	20 — Gnk2 domain, C-X8-C-X2-C motif

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Unit-cell length a length_a	143.400 Å
Unit-cell length b length_b	143.400 Å
Unit-cell length c length_c	143.400 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	48

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.597 Å
Low-resolution limit resolution_low	19.886 Å
R factor r_factor	0.2511
R_work r_work	0.2492
R_free r_free	0.2885

Crystal structure of Gnk2 complexed with mannose

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

Antifungal protein ginkbilobin-2

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

4xre__assembly_1__model_1

4xre__assembly_1__model_1 | I(q)

4xre__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Gnk2 complexed with mannose

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

Antifungal protein ginkbilobin-2

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

4xre__assembly_1__model_1

4xre__assembly_1__model_1 | I(q)

4xre__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)