5ogn

Metalacarborane inhibitors of Carbonic Anhydrase IX

Method: X-RAY DIFFRACTION Dmax: 81.8 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 3–260 Not recorded ZN ZINC ION × 2 B8B cobaltcarborane × 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-HCl pH 7.8 Resolution 1.10 Å R-free 0.202
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 3–260 Not recorded ZN ZINC ION × 1 B8B cobaltcarborane × 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-HCl pH 7.8 Resolution 1.10 Å R-free 0.202

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 1271 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 2–259; UniProt 3–260 Author chain B; PDBConstruct 2–259; UniProt 3–260

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 5ogn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5ogn
Deposition date deposition_date2017-07-13
Structure title titleMetalacarborane inhibitors of Carbonic Anhydrase IX
Keywords keywordsCarbonic Anhydrase IX, 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_guinier25.18
Radius of gyration Rg (electron density) rg_electron24.34
Forward intensity I(0) i053151500.00
Molecular weight molecular_weight58592.0 kDa
Excluded volume excluded_volume73782 ų
Envelope volume envelope_volume85586 ų
Hydration-shell volume shell_volume29171 ų
Envelope diameter envelope_diameter87.5
Shell Rg shell_rg31.90
Envelope Rg envelope_rg24.66
Shape Rg shape_rg24.30
Total Rg total_rg25.32
Total atoms total_atoms4145
Residues n_residues517
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 dmax81.8
Rg (real space) rg_real25.18
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real5.3150e+07
I(0) uncertainty (real space) i0_real_error7.4870e+05
Rg (reciprocal space) rg_reciprocal25.18
I(0) (reciprocal space) i0_reciprocal53150000.0000
Solution quality estimate total_estimate0.8845
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.394
Kurtosis Kurtosis kurtosis-0.276
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10260000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5ogna1
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_idd5ogna2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5ognb_
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_id5ognA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology200 — Carbonic Anhydrase II
Homologous superfamily homologous superfamily10 — Alpha carbonic anhydrase
Domain ID domain_id5ognB00
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)