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2db4

Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae

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

V-Type Sodium ATPase Subunit K

Enterococcus hirae

UniProt P43457

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 10 DICYCLOHEXYLUREA × 10 SODIUM ION × 10 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 20 UNDECYL-MALTOSIDE × 10 water × 10 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2bl2 2cyd 2db4 3aou

4 assemblies

Heteromeric or nucleic-acid complex
8wci

1 assemblies

View Construct and Data Evidence
UniProt name NTPK_ENTHR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–156； UniProt 1–156 Author chain B； PDBConstruct 1–156； UniProt 1–156 Author chain C； PDBConstruct 1–156； UniProt 1–156 Author chain D； PDBConstruct 1–156； UniProt 1–156 Author chain E； PDBConstruct 1–156； UniProt 1–156 Author chain F； PDBConstruct 1–156； UniProt 1–156 Author chain G； PDBConstruct 1–156； UniProt 1–156 Author chain H； PDBConstruct 1–156； UniProt 1–156 Author chain I； PDBConstruct 1–156； UniProt 1–156 Author chain J； PDBConstruct 1–156； UniProt 1–156

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_id2db4
Deposition date deposition_date2005-12-15
Structure title titleCrystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae
Keywords keywords;NtpK, V-ATPase, Na(+)-ATPase, DCCD, Proteolipid, Enterococcus hirae, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE ;; HYDROLASE
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.

2db4__assembly_1__model_1

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

Download this curve (.dat)

2db4__assembly_1__model_1 | I(q)

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

2db4__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）37.06 Å
Rg (electron density)35.27 Å
Total Rg35.95 Å
Atom count12404
Residues1560
Excluded volume234480 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2db4__assembly_1__model_1 decameric （10） 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 (6)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id2db4A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4C00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4D00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4E00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4F00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4G00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4H00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4I00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
Domain ID domain_id2db4J00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily610 — lithium bound rotor ring of v- atpase
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7. Citations (1)