4e3h

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors

Method: X-RAY DIFFRACTION Dmax: 58.6 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 MBO MERCURIBENZOIC ACID × 1 HQE benzene-1,4-diol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;291 K;3M ammonium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 1.50 Å R-free 0.212

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 4e3h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e3h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e3h
Deposition date deposition_date2012-03-09
Structure title titleNucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors
Keywords keywordsCarbonate dehydratase, Inhibitor, 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_guinier18.62
Radius of gyration Rg (electron density) rg_electron17.34
Forward intensity I(0) i015092700.00
Molecular weight molecular_weight29387.0 kDa
Excluded volume excluded_volume36738 ų
Envelope volume envelope_volume40929 ų
Hydration-shell volume shell_volume19131 ų
Envelope diameter envelope_diameter59.9
Shell Rg shell_rg24.13
Envelope Rg envelope_rg17.72
Shape Rg shape_rg17.31
Total Rg total_rg18.43
Total atoms total_atoms2068
Residues n_residues257
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 dmax58.6
Rg (real space) rg_real18.47
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real1.5090e+07
I(0) uncertainty (real space) i0_real_error1.7460e+05
Rg (reciprocal space) rg_reciprocal18.49
I(0) (reciprocal space) i0_reciprocal15090000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.055
Kurtosis Kurtosis kurtosis-0.455
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2277000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.988

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_idd4e3ha_
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_id4e3hA00
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)