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3vkg

X-ray structure of an MTBD truncation mutant of dynein motor domain

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynein heavy chain, cytoplasmic

Dictyostelium discoideum

UniProt P34036

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 ADENOSINE-5'-DIPHOSPHATE × 8 SPERMINE × 4 MAGNESIUM ION × 3 water × 2 Consistent with protein count
2 Protein monomer Monomer Protein 1 ADENOSINE-5'-DIPHOSPHATE × 4 SPERMINE × 2 MAGNESIUM ION × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ADENOSINE-5'-DIPHOSPHATE × 4 SPERMINE × 2 MAGNESIUM ION × 2 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3vkg 3vkg 3vkh 3vkh

4 assemblies

Homodimer
3vkg

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3j6p

1 assemblies

View Construct and Data Evidence
UniProt name DYHC_DICDI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 25–2008； UniProt 1388–3371 Author chain A； PDBConstruct 2011–3245； UniProt 3496–4730 Author chain B； PDBConstruct 25–2008； UniProt 1388–3371 Author chain B； PDBConstruct 2011–3245； UniProt 3496–4730

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_id3vkg
Deposition date deposition_date2011-11-16
Structure title titleX-ray structure of an MTBD truncation mutant of dynein motor domain
Keywords keywordsAAA+ protein, molecular motor, microtubles, motor protein; MOTOR PROTEIN
Experimental Method methodX-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.

3vkg__assembly_1__model_1

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

Download this curve (.dat)

3vkg__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3vkg__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）68.47 Å
Rg (electron density)68.33 Å
Total Rg68.37 Å
Atom count45242
Residues5807
Excluded volume805300 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3vkg__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3vkg__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3vkg__assembly_3__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 (5)

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6. Fold Classification (SCOP + CATH) 25 domains

CATH v4.4 (25 domains)

Domain ID domain_id3vkgA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily100 — Dynein motor heavy chain, linker domain, N-terminal subdomain
Domain ID domain_id3vkgA03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology180 — Split barrel-like
Homologous superfamily homologous superfamily20 — Dynein motor heavy chain, linker domain, subdomain 3
Domain ID domain_id3vkgA04
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1120 — Dynein motor heavy chain, linker domain, subdomain 4
Domain ID domain_id3vkgA05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily710 — Dynein motor, AAA1 domain, small subdomain
Domain ID domain_id3vkgA07
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgA08
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily130 — Dynein motor, AAA2 domain, small subdomain
Domain ID domain_id3vkgA09
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3vkgA10
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgA11
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3vkgA12
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily2610 —
Domain ID domain_id3vkgA13
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgA14
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1060 —
Domain ID domain_id3vkgA15
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1220 —
Domain ID domain_id3vkgA17
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgA18
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily720 — Region D6 of dynein motor
Domain ID domain_id3vkgA20
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology490 — Hypothetical upf0131 protein ytfp
Homologous superfamily homologous superfamily20 — Dynein motor C sequence, barrel region
Domain ID domain_id3vkgB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily100 — Dynein motor heavy chain, linker domain, N-terminal subdomain
Domain ID domain_id3vkgB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology180 — Split barrel-like
Homologous superfamily homologous superfamily20 — Dynein motor heavy chain, linker domain, subdomain 3
Domain ID domain_id3vkgB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1120 — Dynein motor heavy chain, linker domain, subdomain 4
Domain ID domain_id3vkgB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily710 — Dynein motor, AAA1 domain, small subdomain
Domain ID domain_id3vkgB05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3vkgB06
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3vkgB07
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily720 — Region D6 of dynein motor
Domain ID domain_id3vkgB08
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology490 — Hypothetical upf0131 protein ytfp
Homologous superfamily homologous superfamily20 — Dynein motor C sequence, barrel region
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7. Citations (1)