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2dy9

Crystal structure of nucleoside diphosphate kinase in complex with ADP

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

Nucleoside diphosphate kinase

Pyrococcus horikoshii

UniProt O58429

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 MAGNESIUM ION × 3 CHLORIDE ION × 12 ADENOSINE-5'-DIPHOSPHATE × 3 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2cwk

1 assemblies

Homotetramer

None

Other homooligomers
2cwk 2dxd 2dxd 2dxe 2dxf 2dy9 2dya

7 assemblies

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name NDK_PYRHO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–160； UniProt 1–157 Author chain B； PDBConstruct 4–160； UniProt 1–157

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_id2dy9
Deposition date deposition_date2006-09-08
Structure title titleCrystal structure of nucleoside diphosphate kinase in complex with ADP
Keywords keywords;nucleoside binding, kinase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSFERASE ;; TRANSFERASE
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.

2dy9__assembly_1__model_1

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

Download this curve (.dat)

2dy9__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.

2dy9__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）28.81 Å
Rg (electron density)27.62 Å
Total Rg28.37 Å
Atom count7575
Residues930
Excluded volume136280 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2dy9__assembly_1__model_1 hexameric （6） 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2dy9a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.6 — Nucleoside diphosphate kinase, NDK
Family Family familyd.58.6.1 — Nucleoside diphosphate kinase, NDK
Domain ID domain_idd2dy9b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.6 — Nucleoside diphosphate kinase, NDK
Family Family familyd.58.6.1 — Nucleoside diphosphate kinase, NDK

CATH v4.4 (2 domains)

Domain ID domain_id2dy9A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily141 — Nucleoside diphosphate kinase-like domain
Domain ID domain_id2dy9B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily141 — Nucleoside diphosphate kinase-like domain
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7. Citations (1)