6gcy

Joint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (saccharin-sugar conjugate complex)

Dmax: 59.9 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 3QR [1-(1,1-dioxido-3-oxo-2,3-dihydro-1,2-benzothiazol-6-yl)-1H-1,2,3-triazol-4-yl]methyl alpha-L-idopyranoside × 1 Experimental method not declared X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;1.2 M sodium citrate, 0.1 M Tris pH 8.5 in Hampton sandwich box set-ups. Drops were 150-250 uL and we set-up in a 1:1 ratio. To get the complex with SGC ligand we did "dry co-crystallization". Resolution not provided

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 6gcy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gcy
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6gcy
Deposition date deposition_date2018-04-20
Structure title titleJoint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (saccharin-sugar conjugate complex)
Keywords keywordsproton transfer, carbonic anhydrase, LYASE; LYASE

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

Radius of gyration Rg (Guinier) rg_guinier19.21
Radius of gyration Rg (electron density) rg_electron17.82
Forward intensity I(0) i020430500.00
Molecular weight molecular_weight33787.0 kDa
Excluded volume excluded_volume41556 ų
Envelope volume envelope_volume48699 ų
Hydration-shell volume shell_volume21524 ų
Envelope diameter envelope_diameter63.8
Shell Rg shell_rg25.37
Envelope Rg envelope_rg18.46
Shape Rg shape_rg18.15
Total Rg total_rg17.87
Total atoms total_atoms4714
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 dmax59.9
Rg (real space) rg_real19.04
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real2.0430e+07
I(0) uncertainty (real space) i0_real_error2.2680e+05
Rg (reciprocal space) rg_reciprocal19.07
I(0) (reciprocal space) i0_reciprocal20430000.0000
Solution quality estimate total_estimate0.8145
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.056
Kurtosis Kurtosis kurtosis-0.475
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3750000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.868; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6gcya_
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_id6gcyA00
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)