SAXSdb — 3zkf

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

DYNEIN LIGHT CHAIN 1, CYTOPLASMIC

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NEK9 PROTEIN × 2 （Q6PKF2） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	NEK9 PROTEIN × 2 （Q6PKF2） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	NEK9 PROTEIN × 2 （Q6PKF2） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 1–89 Author chain C； PDBConstruct 1–89； UniProt 1–89 Author chain E； PDBConstruct 1–89； UniProt 1–89 Author chain G； PDBConstruct 1–89； UniProt 1–89 Author chain I； PDBConstruct 1–89； UniProt 1–89 Author chain K； PDBConstruct 1–89； UniProt 1–89

NEK9 PROTEIN

OrganismNot specified

UniProt Q6PKF2

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 （P63167） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DYNEIN LIGHT CHAIN 1, CYTOPLASMIC × 2 （P63167） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	DYNEIN LIGHT CHAIN 1, CYTOPLASMIC × 2 （P63167） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6PKF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 283–293 Author chain D； PDBConstruct 1–11； UniProt 283–293 Author chain F； PDBConstruct 1–11； UniProt 283–293 Author chain H； PDBConstruct 1–11； UniProt 283–293 Author chain J； PDBConstruct 1–11； UniProt 283–293 Author chain L； PDBConstruct 1–11； UniProt 283–293

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	3zkf
Deposition date deposition_date	2013-01-22
Structure title title	Structure of LC8 in complex with Nek9 phosphopeptide
Keywords keywords	CONTRACTILE PROTEIN-PEPTIDE COMPLEX; CONTRACTILE PROTEIN/PEPTIDE
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.

3zkf__assembly_1__model_1

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

Download this curve (.dat)

3zkf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zkf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.94 Å
Rg (electron density)	15.73 Å
Total Rg	16.92 Å
Atom count	1559
Residues	190
Excluded volume	27711 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zkf__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zkf__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3zkf__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 (3)

Entity 1 Entity 1 polymer

Description description	DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
Molecular weight formula_weight	10381.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	4658

MCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG

Source Source

Source organism organism	HOMO SAPIENS
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	NEK9 PROTEIN
Molecular weight formula_weight	1198.2 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

VGMHSKGTQTA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3zkfA00
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	3zkfC00
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	3zkfE00
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	3zkfG00
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	3zkfI00
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	3zkfK00
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;

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Unit-cell length a length_a	154.868 Å
Unit-cell length b length_b	154.868 Å
Unit-cell length c length_c	47.729 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	44.967 Å
R factor r_factor	0.2222
R_work r_work	0.2196
R_free r_free	0.2686

Structure of LC8 in complex with Nek9 phosphopeptide

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

NEK9 PROTEIN

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

3zkf__assembly_1__model_1

3zkf__assembly_1__model_1 | I(q)

3zkf__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of LC8 in complex with Nek9 phosphopeptide

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

NEK9 PROTEIN

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

3zkf__assembly_1__model_1

3zkf__assembly_1__model_1 | I(q)

3zkf__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)