SAXSdb — 4p2t

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

KSHV Protease

Human herpesvirus 8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide × 1 DIMETHYL SULFOXIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide × 2 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide × 6 DIMETHYL SULFOXIDE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O36607_HHV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 3–196 Author chain B； PDBConstruct 1–194； UniProt 3–196

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	4p2t
Deposition date deposition_date	2014-03-04
Structure title title	Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with a dimer disruptor
Keywords keywords	protein-protein interaction inhibition, serine protease, inhibitor complex, beta barrel and alpha helices, HYDROLASE; HYDROLASE
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.

4p2t__assembly_1__model_1

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

Download this curve (.dat)

4p2t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p2t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.08 Å
Rg (electron density)	16.65 Å
Total Rg	17.81 Å
Atom count	3036
Residues	192
Excluded volume	27369 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p2t__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4p2t__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4p2t__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 (4)

Entity 1 Entity 1 polymer

Description description	KSHV Protease
Molecular weight formula_weight	21321.2 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	6440

QGLYVGGFVDVVSCPKLEQELYLDPDQVTDYLPVTEPLPITIEHLPETEVGWTLGLFQVSHGIFCTGAITSPAFLELASRLADTSHVARAPVKNLPKEPLLEILHTWLPGLSLSSIHPRELSQTPSGPVFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTPNFVSPLETL

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

Entity 2 Entity 2 non-polymer

Description description	6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide
Molecular weight formula_weight	505.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4p2tA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	4p2tB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

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Unit-cell length a length_a	69.737 Å
Unit-cell length b length_b	95.947 Å
Unit-cell length c length_c	119.245 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 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	74.753 Å
R factor r_factor	0.1911
R_work r_work	0.1852
R_free r_free	0.2523

Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with a dimer disruptor

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

KSHV Protease

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

4p2t__assembly_1__model_1

4p2t__assembly_1__model_1 | I(q)

4p2t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with a dimer disruptor

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

KSHV Protease

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

4p2t__assembly_1__model_1

4p2t__assembly_1__model_1 | I(q)

4p2t__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)