SAXSdb — 2pnq

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

[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDP1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–467； UniProt 72–538 Author chain B； PDBConstruct 1–467； UniProt 72–538

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	2pnq
Deposition date deposition_date	2007-04-25
Structure title title	Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)
Keywords keywords	pyruvate dehydrogenase phosphatase 1, catalytic subunit, PDP1c, 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.

2pnq__assembly_1__model_1

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

Download this curve (.dat)

2pnq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pnq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.48 Å
Rg (electron density)	21.33 Å
Total Rg	22.26 Å
Atom count	3043
Residues	382
Excluded volume	53784 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pnq__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2pnq__assembly_2__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	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
Molecular weight formula_weight	52682.2 kDa
EC 编号 ec_number	3.1.3.43
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	6565

ASTPQKFYLTPPQVNSILKANEYSFKVPEFDGKNVSSILGFDSNRLPANAPIEDRRSATTCLQTRGMLLGVFDGHAGCACSQAVSERLFYYIAVSLLPHETLLEIENAVESGRALLPILQWHKHPNDYFSKEASKLYFNGLRTYWQELIDLNTGESADIDVKEALINAFKRLDNDISLEAQVGDPNSFLNYLVLRVAFSGATACVAHVDGVDLHVANTGDSRAMLGVQEEDGSWSAVTLSNDHNAQNERELQRLKLEHPKNEAKSVVKQDRLLGLLMPFRAFGDVKFKWSIDLQKRVIESGPDQLNDNEYTKFIPPNYHTPPYLTAEPEVTYHRLRPQDKFLVLATDGLWETMHRQDVVRIVGEYLTGMHHQQPIAVGGYKVTLGQMHGLLTERRAKMSSVFEDQNAATHLIRHAVGNNEFGAVDHERLSKMLSLPEELARMYRDDITIIVVQFNSHVVGAYQNQEQ

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	479

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2pnqA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

Domain ID domain_id	2pnqB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	40 — Phosphatase 2c; domain 1
Homologous superfamily homologous superfamily	10 — PPM-type phosphatase domain

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Unit-cell length a length_a	65.318 Å
Unit-cell length b length_b	72.220 Å
Unit-cell length c length_c	96.094 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	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2180
R_work r_work	0.2150
R_free r_free	0.2560

Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)

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

[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1

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

2pnq__assembly_1__model_1

2pnq__assembly_1__model_1 | I(q)

2pnq__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)

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

[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1

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

2pnq__assembly_1__model_1

2pnq__assembly_1__model_1 | I(q)

2pnq__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)