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2cwk

Crystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii

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 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 6 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 1–160； UniProt 1–160 Author chain B； PDBConstruct 1–160； UniProt 1–160

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_id2cwk
Deposition date deposition_date2005-06-21
Structure title titleCrystal structure of nucleotide diphosphate kinase from Pyrococcus horikoshii
Keywords keywords;transferase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2cwk__assembly_1__model_1

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

Download this curve (.dat)

2cwk__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2cwk__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）21.11 Å
Rg (electron density)19.77 Å
Total Rg20.67 Å
Atom count2459
Residues305
Excluded volume44347 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2cwk__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2cwk__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2cwka1
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_idd2cwkb_
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_id2cwkA00
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_id2cwkB00
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)