3iwx

Crystal structure of cisplatin bound to a human copper chaperone (dimer)

Method: X-RAY DIFFRACTION Dmax: 58.2 Å Quality: GOOD

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

Copper transport protein ATOX1

Homo sapiens

UniProt O00244

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–68 Chain B; UniProt 1–68 Not recorded CPT Cisplatin × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;294 K;1.5 M lithium sulfate, 0.1M MES, 50 mM NaCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.14 Å R-free 0.228

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.

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATOX1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–68; UniProt 1–68 Author chain B; PDBConstruct 1–68; UniProt 1–68

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 3iwx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3iwx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3iwx
Deposition date deposition_date2009-09-03
Structure title titleCrystal structure of cisplatin bound to a human copper chaperone (dimer)
Keywords keywords;beta-alpha-beta-beta-alpha-beta, transport protein, cisplatin, platinum, Chaperone, Copper transport, Ion transport, Metal-binding, Transport, METAL TRANSPORT ;; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.51
Radius of gyration Rg (electron density) rg_electron15.66
Forward intensity I(0) i04791080.00
Molecular weight molecular_weight15041.0 kDa
Excluded volume excluded_volume18481 ų
Envelope volume envelope_volume21021 ų
Hydration-shell volume shell_volume11956 ų
Envelope diameter envelope_diameter57.2
Shell Rg shell_rg20.59
Envelope Rg envelope_rg16.03
Shape Rg shape_rg15.71
Total Rg total_rg16.39
Total atoms total_atoms1029
Residues n_residues134
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 dmax58.2
Rg (real space) rg_real16.55
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real4.7910e+06
I(0) uncertainty (real space) i0_real_error6.0640e+04
Rg (reciprocal space) rg_reciprocal16.54
I(0) (reciprocal space) i0_reciprocal4791000.0000
Solution quality estimate total_estimate0.8435
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.4
Skewness Skewness skewness0.392
Kurtosis Kurtosis kurtosis-0.238
Angular range angular_range— – 0.4800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha636600.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.949

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3iwxa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain
Domain ID domain_idd3iwxb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain

CATH v4.4 (2 domains)

Domain ID domain_id3iwxA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100
Domain ID domain_id3iwxB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100

8. Citations (1)

9. Files and Curves (10)