3pyk

Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor

Method: X-RAY DIFFRACTION Dmax: 58.4 Å Quality: GOOD

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

Carbonic anhydrase 2

Homo sapiens

UniProt P00918

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 1–260 Mutation:S2A ZN ZINC ION × 1 SRX chloro{N-[di(pyridin-2-yl-kappaN)methyl]-4-sulfamoylbenzamide}[(1,2,3,4,5,6-eta)-(1R,2R,3R,4S,5S,6S)-1,2,3,4,5,6-hexamethylcyclohexane-1,2,3,4,5,6-hexayl]ruthenium(2+) × 1 MMC METHYL MERCURY ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;3 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed and equilibrated against 500 uL precipitating buffer. Single crystals were transferred into a cross-linking buffer, which was prepared from 10 uL precipitating buffer and 5 uL glutaraldehyde solution (0.8 % glutaraldehyde, 4 M ammonium sulfate, 50 mM Tris-sulfate) and equilibrated for 18 h. Cross-linked crystals were transferred into soaking buffer (9 uL precipitating buffer, 0.5 uL 60 mM {(6-benzene)Ru(bispy 3)Cl}+ in DMSO) and equilibrated for 54 h, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.30 Å R-free 0.165

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.

1239 other PDB entries and 1272 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAH2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–260; UniProt 1–260

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 3pyk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3pyk
Deposition date deposition_date2010-12-13
Structure title titleHuman Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor
Keywords keywords;10 STRANDED, TWISTED BETA-SHEETS, carbonate dehydratase activity, protein binding, zinc ion binding, lyase activity, metal ion binding, CO2, bicarbonate, sulfonamides, metal ions, LYASE-LYASE INHIBITOR complex ;; LYASE/LYASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.52
Radius of gyration Rg (electron density) rg_electron17.29
Forward intensity I(0) i015927300.00
Molecular weight molecular_weight30054.0 kDa
Excluded volume excluded_volume37448 ų
Envelope volume envelope_volume41653 ų
Hydration-shell volume shell_volume19445 ų
Envelope diameter envelope_diameter60.9
Shell Rg shell_rg24.18
Envelope Rg envelope_rg17.71
Shape Rg shape_rg17.27
Total Rg total_rg18.35
Total atoms total_atoms2106
Residues n_residues258
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 dmax58.4
Rg (real space) rg_real18.38
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real1.5930e+07
I(0) uncertainty (real space) i0_real_error1.7550e+05
Rg (reciprocal space) rg_reciprocal18.40
I(0) (reciprocal space) i0_reciprocal15930000.0000
Solution quality estimate total_estimate0.8080
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.0
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3078000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3pyka_
Class classb — All beta proteins
Fold Fold foldb.74 — Carbonic anhydrase
Superfamily Superfamily superfamilyb.74.1 — Carbonic anhydrase
Family Family familyb.74.1.1 — Carbonic anhydrase

CATH v4.4 (1 domains)

Domain ID domain_id3pykA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology200 — Carbonic Anhydrase II
Homologous superfamily homologous superfamily10 — Alpha carbonic anhydrase

8. Citations (1)

9. Files and Curves (10)