5e2m

Crystal structure of human carbonic anhydrase isozyme I with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: GOOD

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

Carbonic anhydrase 1

Homo sapiens

UniProt P00915

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 3–261 Fragment:human carbonic anhydrase I ZN ZINC ION × 1 V14 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.4;291 K;Crystallization buffer contains 0.1M TrisHCl (pH 8.5), 0.2M ammonium acetate, 28% of PEG4000 Resolution 1.41 Å R-free 0.207
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 3–261 Fragment:human carbonic anhydrase I ZN ZINC ION × 1 V14 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.4;291 K;Crystallization buffer contains 0.1M TrisHCl (pH 8.5), 0.2M ammonium acetate, 28% of PEG4000 Resolution 1.41 Å R-free 0.207

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.

55 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAH1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–260; UniProt 3–261 Author chain B; PDBConstruct 2–260; UniProt 3–261

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 5e2m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e2m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e2m
Deposition date deposition_date2015-10-01
Structure title titleCrystal structure of human carbonic anhydrase isozyme I with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Keywords keywordsdrug design, carbonic anhydrase, benzenesulfonamide, metal-binding, lyase-lyase inhibitor complex, lyase; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.83
Radius of gyration Rg (electron density) rg_electron31.61
Forward intensity I(0) i054535300.00
Molecular weight molecular_weight57670.0 kDa
Excluded volume excluded_volume71625 ų
Envelope volume envelope_volume89347 ų
Hydration-shell volume shell_volume24059 ų
Envelope diameter envelope_diameter108.2
Shell Rg shell_rg37.61
Envelope Rg envelope_rg31.21
Shape Rg shape_rg31.60
Total Rg total_rg32.13
Total atoms total_atoms4068
Residues n_residues513
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 dmax101.2
Rg (real space) rg_real32.14
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real5.4540e+07
I(0) uncertainty (real space) i0_real_error8.8240e+05
Rg (reciprocal space) rg_reciprocal32.02
I(0) (reciprocal space) i0_reciprocal54530000.0000
Solution quality estimate total_estimate0.7560
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.3
Skewness Skewness skewness0.364
Kurtosis Kurtosis kurtosis-0.877
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12440000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.632; Smooth: 0.655

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5e2ma_
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
Domain ID domain_idd5e2mb_
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 (2 domains)

Domain ID domain_id5e2mA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology200 — Carbonic Anhydrase II
Homologous superfamily homologous superfamily10 — Alpha carbonic anhydrase
Domain ID domain_id5e2mB00
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)