SAXSdb — 2nyz

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

Hypothetical protein GAMMAHV.M3

Murid herpesvirus 4

UniProt O41925

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Lymphotactin × 2 （P47992） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O41925_MHV68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–382； UniProt 25–406 Author chain B； PDBConstruct 1–382； UniProt 25–406

Lymphotactin

OrganismNot specified

UniProt P47992

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Hypothetical protein GAMMAHV.M3 × 2 （O41925） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XCL1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–93； UniProt 22–114 Author chain E； PDBConstruct 1–93； UniProt 22–114

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	2nyz
Deposition date deposition_date	2006-11-21
Structure title title	Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1
Keywords keywords	Viral Decoy Receptor, Chemokine, Protein-Protein Complex, VIRAL PROTEIN-CYTOKINE COMPLEX; VIRAL PROTEIN/CYTOKINE
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.

2nyz__assembly_1__model_1

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

Download this curve (.dat)

2nyz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nyz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.55 Å
Rg (electron density)	30.41 Å
Total Rg	31.10 Å
Atom count	6718
Residues	869
Excluded volume	119570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nyz__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein GAMMAHV.M3
Molecular weight formula_weight	41826.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6912

LTLGLAPALSTHSSGVSTQSVDLSQIKRGDEIQAHCLTPAETEVTECAGILKDVLSKNLHELQGLCNVKNKMGVPWVSVEELGQEIITGRLPFPSVGGTPVNDLVRVLVVAESNTPEETPEEEFYAYVELQTELYTFGLSDDNVVFTSDYMTVWMIDIPKSYVDVGMLTRATFLEQWPGAKVTVMIPYSSTFTWCGELGAISEESAPQPSLSARSPVCKNSARYSTSKFCEVDGCTAETGMEKMSLLTPFGGPPQQAKMNTCPCYYKYSVSPLPAMDHLILADLAGLDSLTSPVYVMAAYFDSTHENPVRPSSKLYHCALQMTSHDGVWTSTSSEQCPIRLVEGQSQNVLQVRVAPTSMPNLVGVSLMLEGQQYRLEYFGDH

Source Source

Source organism organism	Murid herpesvirus 4
Common name common_name	Murine herpesvirus 68
NCBI taxonomy ID ncbi_taxonomy_id	33708
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Lymphotactin
Molecular weight formula_weight	10286.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	194

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nyza1
Class class	b — All beta proteins
Fold Fold fold	b.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamily	b.116.1 — Viral chemokine binding protein m3
Family Family family	b.116.1.1 — Viral chemokine binding protein m3

Domain ID domain_id	d2nyzb1
Class class	b — All beta proteins
Fold Fold fold	b.116 — Viral chemokine binding protein m3
Superfamily Superfamily superfamily	b.116.1 — Viral chemokine binding protein m3
Family Family family	b.116.1.1 — Viral chemokine binding protein m3

CATH v4.4 (6 domains)

Domain ID domain_id	2nyzA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1330 —

Domain ID domain_id	2nyzA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1340 — Chemokine-binding protein M3-like

Domain ID domain_id	2nyzB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1330 —

Domain ID domain_id	2nyzB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1340 — Chemokine-binding protein M3-like

Domain ID domain_id	2nyzD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2nyzE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	84.370 Å
Unit-cell length b length_b	103.190 Å
Unit-cell length c length_c	290.940 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2720

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1

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

Hypothetical protein GAMMAHV.M3

State in the Current Structure

Other States of the Same Protein in the Database

Lymphotactin

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

2nyz__assembly_1__model_1

2nyz__assembly_1__model_1 | I(q)

2nyz__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1

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

Hypothetical protein GAMMAHV.M3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lymphotactin

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

2nyz__assembly_1__model_1

2nyz__assembly_1__model_1 | I(q)

2nyz__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)