1ndc

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 53.8 Å Quality: GOOD

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

NUCLEOSIDE DIPHOSPHATE KINASE

Dictyostelium discoideum

UniProt P22887

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–155 Not recorded MG MAGNESIUM ION × 6 TYD THYMIDINE-5'-DIPHOSPHATE × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDKC_DICDI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–155; UniProt 1–155

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1ndc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ndc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ndc
Deposition date deposition_date1994-04-27
Structure title titleX-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION
Keywords keywordsPHOSPHOTRANSFERASE, NUCLEOSIDE TRIPHOSPHATE, NUCLEOSIDE DIPHOSPHATE; PHOSPHOTRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.06
Radius of gyration Rg (electron density) rg_electron14.95
Forward intensity I(0) i05228990.00
Molecular weight molecular_weight16659.0 kDa
Excluded volume excluded_volume20985 ų
Envelope volume envelope_volume23583 ų
Hydration-shell volume shell_volume13419 ų
Envelope diameter envelope_diameter54.0
Shell Rg shell_rg20.80
Envelope Rg envelope_rg15.46
Shape Rg shape_rg14.94
Total Rg total_rg16.09
Total atoms total_atoms1173
Residues n_residues150
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.8
Rg (real space) rg_real16.01
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real5.2290e+06
I(0) uncertainty (real space) i0_real_error5.7360e+04
Rg (reciprocal space) rg_reciprocal16.01
I(0) (reciprocal space) i0_reciprocal5229000.0000
Solution quality estimate total_estimate0.7922
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.4
Skewness Skewness skewness0.305
Kurtosis Kurtosis kurtosis-0.128
Angular range angular_range— – 0.4950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1186000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ndca_
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 (1 domains)

Domain ID domain_id1ndcA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily141 — Nucleoside diphosphate kinase-like domain

8. Citations (3)

9. Files and Curves (10)