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Yorodumi- PDB-1hug: Differences in anionic inhibition of Human Carbonic Anhydrase I r... -
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-Basic information
Entry | Database: PDB / ID: 1hug | ||||||
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Title | Differences in anionic inhibition of Human Carbonic Anhydrase I revealed from the structures of iodide and gold cyanide inhibitor complexes | ||||||
Components | CARBONIC ANHYDRASE ICarbonic anhydrase | ||||||
Keywords | LYASE(OXO-ACID) | ||||||
Function / homology | Function and homology information hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Kumar, V. / Kannan, K.K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Differences in anionic inhibition of human carbonic anhydrase I revealed from the structures of iodide and gold cyanide inhibitor complexes. Authors: Kumar, V. / Kannan, K.K. / Sathyamurthi, P. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1993 Title: Structure of Human Carbonic Anhydrase Complexed with Gold Cyanide Inhibitor: Inhibition Mechanism Authors: Kumar, V. / Kannan, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hug.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hug.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hug ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hug | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202 / 3: HET ATOM ZN IS ESSENTIAL METAL ION. 4: THE RESIDUES DEFINING THE CAT SITE CONSTITUTE THE CATALYTIC ACTIVE SITE OF THE ENZYME. INHIBITOR GOLD CYANIDE ANION BINDS IN THE POCKET DEFINED BY THESE RESIDUES AND ACCEPTS A H-BOND FROM THE ...4: THE RESIDUES DEFINING THE CAT SITE CONSTITUTE THE CATALYTIC ACTIVE SITE OF THE ENZYME. INHIBITOR GOLD CYANIDE ANION BINDS IN THE POCKET DEFINED BY THESE RESIDUES AND ACCEPTS A H-BOND FROM THE ACTIVITY LINKED HYDROXYL GROUP BOUND TO THE ZINC ION. THE CONFORMATIONAL REORIENTATION IN THE HYDROXYL GROUP DUE TO H-BOND WITH THE INHIBITOR ANION, RENDERS THE ENZYME INACTIVE. 5: THE SIDE CHAINS OF RESIDUES ASP 9, LYS 10, ARG 173 AND GLU 221 SHOW VERY POOR ELECTRON DENSITY IN THE FOURIER MAPS. 6: HET ATOM AU 501 IS THE PARTIAL OVERLAPPING BINDING SITE OF THE HET AUC 500 GROUP. |
-Components
#1: Protein | Mass: 28774.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase | ||||||||
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#2: Chemical | ChemComp-ZN / | ||||||||
#3: Chemical | ChemComp-AUC / #4: Water | ChemComp-HOH / | Compound details | THE RESIDUES DEFINING THE CAT SITE CONSTITUTE THE CATALYTIC ACTIVE SITE OF THE ENZYME. INHIBITOR ...THE RESIDUES DEFINING THE CAT SITE CONSTITUTE | Nonpolymer details | ATOM ZN IS ESSENTIAL METAL ION | Sequence details | ON THE BASIS OF HUMAN CARBONIC ANHYDRASE - BICARBONATE COMPLEX STRUCTURE (VINAY KUMAR AND K.K. ...ON THE BASIS OF HUMAN CARBONIC ANHYDRASE - BICARBONAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.93 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.7 / Method: microdialysisDetails: referred to 'Kannan,K.K.', (1972) 'J. Mol. Biol.', 63, 601-604 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å Details: THE POTENTIAL SOLVENT SITES WERE IDENTIFIED FROM FO-FC MAP IF THE PEAK HEIGHT WERE MORE THAN 3 TIMES THE S.D OF THE MAP AND WERE WITHIN THE H-BONDING DISTANCE TO A DONOR/ACCEPTOR ATOM. ...Details: THE POTENTIAL SOLVENT SITES WERE IDENTIFIED FROM FO-FC MAP IF THE PEAK HEIGHT WERE MORE THAN 3 TIMES THE S.D OF THE MAP AND WERE WITHIN THE H-BONDING DISTANCE TO A DONOR/ACCEPTOR ATOM. SOLVENTS WERE ADDED TO THE COORDINATE LIST IF ELECTRON DENSITY WAS ALSO OBSERVED IN (2FO - FC) MAP. IN ADDITION TO POSITIONAL AND ISOTROPIC THERMAL PARAMETER, OCCUPANCY WAS ALSO REFINED FOR THE SOLVENT MOLECULES. SOLVENTS WHICH REFINED TO HIGH B-VALUE (>58A2), LOW OCCUPANCY (<30 PER CENT) WERE NOT INCLUDED IN THE MODEL DURING SUBSEQUENT STAGES OF REFINEMENT. THE SUBMITTED MODEL HAS 231 SOLVENT MOLECULES OUT OF WHICH 70 SOLVENTS ARE WITH PARTIAL OXYGEN OCCUPANCY. THE SIDE CHAINS OF RESIDUES ASP 9, LYS 10, ARG 173 AND GLU 221 SHOW VERY POOR ELECTRON DENSITY IN THE FOURIER MAPS. ATOM AU 501 IS THE PARTIAL OVERLAPPING BINDING SITE OF THE HET AUC 500 GROUP.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(I): 0 / Rfactor obs: 0.171 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |