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Yorodumi- PDB-1ydd: STRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ydd | ||||||
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Title | STRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBONIC ANHYDRASE II | ||||||
Components | CARBONIC ANHYDRASE IICarbonic anhydrase | ||||||
Keywords | HYDRO-LYASE | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Nair, S.K. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structural basis of inhibitor affinity to variants of human carbonic anhydrase II. Authors: Nair, S.K. / Krebs, J.F. / Christianson, D.W. / Fierke, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ydd.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ydd.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1ydd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/1ydd ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1ydd | 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 |
-Components
#1: Protein | Mass: 29201.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HG / |
#4: Chemical | ChemComp-AZM / |
#5: Water | ChemComp-HOH / |
Compound details | SECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, ...SECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, BIOPOLYMER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop / Details: Nair, S. K., (1993) Biochemistry, 32, 4506. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 11425 / Num. measured all: 20609 / Rmerge(I) obs: 0.093 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→6.5 Å / σ(I): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.1→6.5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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