2gnn

Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E

Method: X-RAY DIFFRACTION

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

Vascular endothelial growth factor homolog

Orf virus (strain NZ2)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1 SULFATE ION × 1 BENZAMIDINE × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GLYCEROL × 7 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 SULFATE ION × 1 BENZAMIDINE × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GLYCEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 3 SULFATE ION × 2 BENZAMIDINE × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GLYCEROL × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VEGFH_ORFN2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–119； UniProt 21–133 Author chain B； PDBConstruct 7–119； UniProt 21–133 Author chain C； PDBConstruct 7–119； UniProt 21–133 Author chain D； PDBConstruct 7–119； UniProt 21–133

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	2gnn
Deposition date deposition_date	2006-04-10
Structure title title	Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E
Keywords keywords	VEGF, Orf, S-SAD, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
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.

2gnn__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2gnn__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gnn__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.94 Å
Rg (electron density)	19.05 Å
Total Rg	19.77 Å
Atom count	1444
Residues	183
Excluded volume	25506 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gnn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2gnn__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2gnn__assembly_3__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Vascular endothelial growth factor homolog
Molecular weight formula_weight	14273.1 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	3144

EAEAEFDSNTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVTMELLGASGSGSNGMQRLSFVEHKKCDCRPRFTTTPPTTTRPPRRRRVDHHHHHH

Source Source

Source organism organism	Orf virus (strain NZ2)
NCBI taxonomy ID ncbi_taxonomy_id	10259
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2gnna_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d2gnnb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d2gnnc_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d2gnnd_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2gnnA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	2gnnB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	2gnnC00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	2gnnD00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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Unit-cell length a length_a	98.600 Å
Unit-cell length b length_b	98.600 Å
Unit-cell length c length_c	240.000 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 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.480 Å
R factor r_factor	0.2240
R_work r_work	0.2230
R_free r_free	0.2470

Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E

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

Vascular endothelial growth factor homolog

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

2gnn__assembly_2__model_1

2gnn__assembly_2__model_1 | I(q)

2gnn__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal Structure of the Orf Virus NZ2 Variant of VEGF-E

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

Vascular endothelial growth factor homolog

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

2gnn__assembly_2__model_1

2gnn__assembly_2__model_1 | I(q)

2gnn__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)