SAXSdb — 2pnl

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

Protease VP4

Infectious pancreatic necrosis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GUANIDINE × 2 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	GUANIDINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GUANIDINE × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GUANIDINE × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GUANIDINE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GUANIDINE × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GUANIDINE × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	GUANIDINE × 3 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	GUANIDINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_IPNVS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 514–716 Author chain B； PDBConstruct 1–203； UniProt 514–716 Author chain C； PDBConstruct 1–203； UniProt 514–716 Author chain D； PDBConstruct 1–203； UniProt 514–716 Author chain E； PDBConstruct 1–203； UniProt 514–716 Author chain F； PDBConstruct 1–203； UniProt 514–716 Author chain G； PDBConstruct 1–203； UniProt 514–716 Author chain H； PDBConstruct 1–203； UniProt 514–716 Author chain I； PDBConstruct 1–203； UniProt 514–716 Author chain J； PDBConstruct 1–203； UniProt 514–716

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	2pnl
Deposition date deposition_date	2007-04-24
Structure title title	Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1
Keywords keywords	acyl-enzyme, protease, Ser/Lys dyad, viral protease, substrate complex, product complex, 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.

2pnl__assembly_8__model_1

Assembly 8 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2pnl__assembly_8__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pnl__assembly_8__model_1 | P(r) · Pending

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

Rg（Guinier）	17.96 Å
Rg (electron density)	16.48 Å
Total Rg	17.51 Å
Atom count	1528
Residues	200
Excluded volume	27224 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pnl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2pnl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2pnl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2pnl__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2pnl__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2pnl__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2pnl__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2pnl__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2pnl__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2pnl__assembly_10__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	Protease VP4
Molecular weight formula_weight	21756.2 kDa
Mutation mutation	K674A
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	16426

GKFSRALKNRLESANYEEVELPPPSKGVIVPVVHTVKSAPGEAFGSLAIIIPGEYPELLDANQQVLSHFANDTGSVWGIGEDIPFEGDNMCYTALPLKEIKRNGNIVVEKIFAGPIMGPSAQLGLSLLVNDIEDGVPRMVFTGEIADDEETIIPICGVDIAAIAAHEQGLPLIGNQPGVDEEVRNTSLAAHLIQTGTLPVQRA

Source Source

Source organism organism	Infectious pancreatic necrosis virus
NCBI taxonomy ID ncbi_taxonomy_id	11002
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GUANIDINE
Molecular weight formula_weight	59.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1216

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	2pnlA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2pnlJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	41.703 Å
Unit-cell length b length_b	69.262 Å
Unit-cell length c length_c	191.388 Å
Unit-cell angle α angle_alpha	93.06 °
Unit-cell angle β angle_beta	95.03 °
Unit-cell angle γ angle_gamma	97.56 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	182.570 Å
R factor r_factor	0.1940
R_work r_work	0.1900
R_free r_free	0.2670

Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1

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

Protease VP4

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

2pnl__assembly_8__model_1

2pnl__assembly_8__model_1 | I(q)

2pnl__assembly_8__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (2)

Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1

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

Protease VP4

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

2pnl__assembly_8__model_1

2pnl__assembly_8__model_1 | I(q)

2pnl__assembly_8__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (2)