6yol

Meta-Nidocarborane propyl-sulfonamide in complex with CA IX mimic

Method: X-RAY DIFFRACTION Dmax: 57.8 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 P5T Meta-Nidocarborane propyl-sulfonamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;291 K;1.6 M sodium citrate, 50 mM Tris-H2SO4 Resolution 1.15 Å R-free 0.171

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 6yol

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6yol
Deposition date deposition_date2020-04-14
Structure title titleMeta-Nidocarborane propyl-sulfonamide in complex with CA IX mimic
Keywords keywordsCARBONIC ANHYDRASE, CA INHIBITOR, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.64
Radius of gyration Rg (electron density) rg_electron17.25
Forward intensity I(0) i013809600.00
Molecular weight molecular_weight28619.0 kDa
Excluded volume excluded_volume36029 ų
Envelope volume envelope_volume40051 ų
Hydration-shell volume shell_volume18908 ų
Envelope diameter envelope_diameter59.3
Shell Rg shell_rg23.97
Envelope Rg envelope_rg17.57
Shape Rg shape_rg17.23
Total Rg total_rg18.34
Total atoms total_atoms2028
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 dmax57.8
Rg (real space) rg_real18.49
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real1.3810e+07
I(0) uncertainty (real space) i0_real_error1.6430e+05
Rg (reciprocal space) rg_reciprocal18.51
I(0) (reciprocal space) i0_reciprocal13810000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.043
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1948000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6yola_
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

8. Citations (1)

9. Files and Curves (10)