SAXSdb — 3pkn

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

Polyadenylate-binding protein 1

Homo sapiens

UniProt P11940

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	La-related protein 4 × 1 （Q71RC2） SULFATE ION × 1 IODIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	La-related protein 4 × 2 （Q71RC2） SULFATE ION × 2 IODIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PABP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–88； UniProt 544–626

La-related protein 4

OrganismNot specified

UniProt Q71RC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Polyadenylate-binding protein 1 × 1 （P11940） SULFATE ION × 1 IODIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Polyadenylate-binding protein 1 × 2 （P11940） SULFATE ION × 2 IODIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LARP4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–14； UniProt 13–26

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	3pkn
Deposition date deposition_date	2010-11-11
Structure title title	Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)
Keywords keywords	All helical domain, Protein binding, La-related protein 4; PROTEIN BINDING
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.

3pkn__assembly_1__model_1

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

Download this curve (.dat)

3pkn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pkn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.39 Å
Rg (electron density)	13.13 Å
Total Rg	14.25 Å
Atom count	697
Residues	90
Excluded volume	12536 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pkn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pkn__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Polyadenylate-binding protein 1
Molecular weight formula_weight	9421.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	743

GPLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	La-related protein 4
Molecular weight formula_weight	1541.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TGLNPNAKVWQEIA

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	42

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3pknA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

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Unit-cell length a length_a	48.910 Å
Unit-cell length b length_b	31.384 Å
Unit-cell length c length_c	52.647 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.830 Å
R factor r_factor	0.2268
R_work r_work	0.2248
R_free r_free	0.2693

Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)

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

Polyadenylate-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

La-related protein 4

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

3pkn__assembly_1__model_1

3pkn__assembly_1__model_1 | I(q)

3pkn__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)

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

Polyadenylate-binding protein 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

La-related protein 4

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

3pkn__assembly_1__model_1

3pkn__assembly_1__model_1 | I(q)

3pkn__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)