6gob

X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain

Method: X-RAY DIFFRACTION Dmax: 58.1 Å Quality: GOOD

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

Lysozyme C

OrganismNot specified

UniProt P00698

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–147 Not recorded PD PALLADIUM ION × 2 NO3 NITRATE ION × 2 F6Q N,N-pyridylbenzimidazole derivative-Pd complex × 5 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.4;293 K;20% ethylene glycol 0.1 M sodium acetate pH 4.4 0.6 M sodium nitrate Resolution 1.96 Å R-free 0.231

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.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 19–147

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 6gob

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gob
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6gob
Deposition date deposition_date2018-06-01
Structure title titleX-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain
Keywords keywords;protein-metallodrug interaction, palladium-based drug, N-pyridylbenzimidazole bidentate ligands, stacking, non covalent bond, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.44
Radius of gyration Rg (electron density) rg_electron15.04
Forward intensity I(0) i07844290.00
Molecular weight molecular_weight17253.0 kDa
Excluded volume excluded_volume19957 ų
Envelope volume envelope_volume22951 ų
Hydration-shell volume shell_volume13131 ų
Envelope diameter envelope_diameter57.0
Shell Rg shell_rg20.66
Envelope Rg envelope_rg15.44
Shape Rg shape_rg14.86
Total Rg total_rg16.34
Total atoms total_atoms1144
Residues n_residues129
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 dmax58.1
Rg (real space) rg_real16.37
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real7.8440e+06
I(0) uncertainty (real space) i0_real_error9.4040e+04
Rg (reciprocal space) rg_reciprocal16.38
I(0) (reciprocal space) i0_reciprocal7844000.0000
Solution quality estimate total_estimate0.8491
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.187
Angular range angular_range— – 0.4850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha817800.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6goba_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme

CATH v4.4 (1 domains)

Domain ID domain_id6gobA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)