SAXSdb — 5lde

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

Immunoglobulin G-binding protein G,Viral FLICE protein

Human herpesvirus 8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a × 2 （D3DWY2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VFLIP_HHV8P
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 70–257； UniProt 1–188 Author chain B； PDBConstruct 70–257； UniProt 1–188

Immunoglobulin G-binding protein G,Viral FLICE protein

Human herpesvirus 8

UniProt P19909

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a × 2 （D3DWY2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPG2_STRSG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–55； UniProt 304–356 Author chain B； PDBConstruct 3–55； UniProt 304–356

Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a

OrganismNot specified

UniProt D3DWY2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Immunoglobulin G-binding protein G,Viral FLICE protein × 2 （F5HEZ4,P19909）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3DWY2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 1–20； UniProt 45–64 Author chain S； PDBConstruct 1–20； UniProt 45–64

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	5lde
Deposition date deposition_date	2016-06-24
Structure title title	Crystal structure of a vFLIP-IKKgamma stapled peptide dimer
Keywords keywords	vFLIP, NF-kB, Nemo, viral protein; VIRAL 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.

5lde__assembly_1__model_1

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

Download this curve (.dat)

5lde__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lde__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.21 Å
Rg (electron density)	33.47 Å
Total Rg	34.15 Å
Atom count	3463
Residues	482
Excluded volume	61514 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lde__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 (2)

Entity 1 Entity 1 polymer

Description description	Immunoglobulin G-binding protein G,Viral FLICE protein
Molecular weight formula_weight	30194.5 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	3463

MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTELEVLFQGPLDPNSMATYEVLCEVARKLGTDDREVVLFLLNVFIPQPTLAQLIGALRALKEEGRLTFPLLAECLFRAGRRDLLRDLLHLDPRFLERHLAGTMSYFSPYQLTVLHVDGELCARDIRSLIFLSKDTIGSRSTPQTFLHWVYCMENLDLLGPTDVDALMSMLRSLSRVDLQRQVQTLMGLHLSGPSHSQHYRHTPLEHHHHHH

Source Source

Source organism organism	Human herpesvirus 8
Common name common_name	HHV-8
NCBI taxonomy ID ncbi_taxonomy_id	37296
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a
Molecular weight formula_weight	2367.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S

LQVAYHXLFQXYDNHIKSSC

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5ldeA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5ldeA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5ldeA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5ldeB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5ldeB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5ldeB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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Unit-cell length a length_a	90.510 Å
Unit-cell length b length_b	90.510 Å
Unit-cell length c length_c	134.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.380 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2570
R_work r_work	0.2550
R_free r_free	0.2900

Crystal structure of a vFLIP-IKKgamma stapled peptide dimer

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

Immunoglobulin G-binding protein G,Viral FLICE protein

State in the Current Structure

Other States of the Same Protein in the Database

Immunoglobulin G-binding protein G,Viral FLICE protein

State in the Current Structure

Other States of the Same Protein in the Database

Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a

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

5lde__assembly_1__model_1

5lde__assembly_1__model_1 | I(q)

5lde__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of a vFLIP-IKKgamma stapled peptide dimer

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

Immunoglobulin G-binding protein G,Viral FLICE protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Immunoglobulin G-binding protein G,Viral FLICE protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, isoform CRA_a

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

5lde__assembly_1__model_1

5lde__assembly_1__model_1 | I(q)

5lde__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)