5u0d

Identification of a New Zinc Binding Chemotype by Fragment Screening

Method: X-RAY DIFFRACTION Dmax: 59.3 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 Not recorded ZN ZINC ION × 1 7R7 (5R)-5-(2,4-dimethoxyphenyl)-2-sulfanylidene-1,3-oxazolidin-4-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;281 K;the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection Resolution 1.59 Å R-free 0.154

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 5u0d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5u0d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5u0d
Deposition date deposition_date2016-11-23
Structure title titleIdentification of a New Zinc Binding Chemotype by Fragment Screening
Keywords keywordsFragment screening, carbonic anhydrase, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.65
Radius of gyration Rg (electron density) rg_electron17.37
Forward intensity I(0) i014927700.00
Molecular weight molecular_weight29438.0 kDa
Excluded volume excluded_volume36951 ų
Envelope volume envelope_volume41374 ų
Hydration-shell volume shell_volume19279 ų
Envelope diameter envelope_diameter60.8
Shell Rg shell_rg24.20
Envelope Rg envelope_rg17.79
Shape Rg shape_rg17.33
Total Rg total_rg18.48
Total atoms total_atoms2083
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 dmax59.3
Rg (real space) rg_real18.50
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real1.4930e+07
I(0) uncertainty (real space) i0_real_error1.9180e+05
Rg (reciprocal space) rg_reciprocal18.53
I(0) (reciprocal space) i0_reciprocal14930000.0000
Solution quality estimate total_estimate0.8886
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.5
Skewness Skewness skewness0.078
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2683000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.986

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5u0da_
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_id5u0dA00
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)