SAXSdb — 3dvp

▼

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

Dynein light chain 1, cytoplasmic

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	P21 activated Kinase peptide × 2 （Q13153） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYL1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–91； UniProt 1–89 Author chain B； PDBConstruct 3–91； UniProt 1–89

P21 activated Kinase peptide

OrganismNot specified

UniProt Q13153

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Dynein light chain 1, cytoplasmic × 2 （Q24117） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAK1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 212–221 Author chain D； PDBConstruct 1–10； UniProt 212–221

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dvp
Deposition date deposition_date	2008-07-18
Structure title title	Pak1 peptide bound LC8
Keywords keywords	Pak1, LC8, DLC1, PIN, Complex, Dynein, Microtubule, Motor protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN, MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3dvp__assembly_1__model_1

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

Download this curve (.dat)

3dvp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dvp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.77 Å
Rg (electron density)	15.54 Å
Total Rg	16.70 Å
Atom count	1516
Residues	188
Excluded volume	26951 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dvp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Dynein light chain 1, cytoplasmic
Molecular weight formula_weight	10603.1 kDa
Mutation mutation	K36P
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	1565

MDMSDRKAVIKNADMSEEMQQDAVDCATQALEKYNIEPDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	P21 activated Kinase peptide
Molecular weight formula_weight	1045.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

TPTRDVATSP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dvpa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.39 — DLC
Superfamily Superfamily superfamily	d.39.1 — DLC
Family Family family	d.39.1.1 — DLC

Domain ID domain_id	d3dvpb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.39 — DLC
Superfamily Superfamily superfamily	d.39.1 — DLC
Family Family family	d.39.1.1 — DLC

CATH v4.4 (2 domains)

Domain ID domain_id	3dvpA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

Domain ID domain_id	3dvpB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

▶

Unit-cell length a length_a	47.404 Å
Unit-cell length b length_b	57.378 Å
Unit-cell length c length_c	64.801 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	11.650 Å
R factor r_factor	0.2069
R_work r_work	0.2040
R_free r_free	0.2628

Pak1 peptide bound LC8

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

Dynein light chain 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

P21 activated Kinase peptide

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

3dvp__assembly_1__model_1

3dvp__assembly_1__model_1 | I(q)

3dvp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Pak1 peptide bound LC8

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

Dynein light chain 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

P21 activated Kinase peptide

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

3dvp__assembly_1__model_1

3dvp__assembly_1__model_1 | I(q)

3dvp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)