5gmm

Crystal structure of human Carbonic anhydrase I in complex with polmacoxib

Method: X-RAY DIFFRACTION Dmax: 82.5 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 1–261 Not recorded ZN ZINC ION × 1 949 4-[3-(3-fluorophenyl)-5,5-dimethyl-4-oxidanylidene-furan-2-yl]benzenesulfonamide × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;0.1 M HEPES pH 6.7~8.2, 0.5~1.4 M tri-Na citrate. Resolution 2.00 Å R-free 0.227
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–261 Not recorded ZN ZINC ION × 2 949 4-[3-(3-fluorophenyl)-5,5-dimethyl-4-oxidanylidene-furan-2-yl]benzenesulfonamide × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;0.1 M HEPES pH 6.7~8.2, 0.5~1.4 M tri-Na citrate. Resolution 2.00 Å R-free 0.227

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 1–261; UniProt 1–261 Author chain B; PDBConstruct 1–261; UniProt 1–261

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 5gmm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5gmm
Deposition date deposition_date2016-07-14
Structure title titleCrystal structure of human Carbonic anhydrase I in complex with polmacoxib
Keywords keywordsLyase, Inhibitor, Complex; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.99
Radius of gyration Rg (electron density) rg_electron24.10
Forward intensity I(0) i059527500.00
Molecular weight molecular_weight59294.0 kDa
Excluded volume excluded_volume73692 ų
Envelope volume envelope_volume85388 ų
Hydration-shell volume shell_volume29383 ų
Envelope diameter envelope_diameter84.4
Shell Rg shell_rg31.65
Envelope Rg envelope_rg24.25
Shape Rg shape_rg24.06
Total Rg total_rg25.06
Total atoms total_atoms4183
Residues n_residues514
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 dmax82.5
Rg (real space) rg_real24.97
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real5.9530e+07
I(0) uncertainty (real space) i0_real_error8.1390e+05
Rg (reciprocal space) rg_reciprocal24.98
I(0) (reciprocal space) i0_reciprocal59530000.0000
Solution quality estimate total_estimate0.8800
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.261
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11860000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.948

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5gmma_
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_idd5gmmb_
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_id5gmmA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology200 — Carbonic Anhydrase II
Homologous superfamily homologous superfamily10 — Alpha carbonic anhydrase
Domain ID domain_id5gmmB00
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)