+Open data
-Basic information
Entry | Database: PDB / ID: 2nmx | ||||||
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Title | Structure of inhibitor binding to Carbonic Anhydrase I | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / metalloenzyme / hydro lyase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Christianson, D.W. / Jude, K.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Structural Analysis of Charge Discrimination in the Binding of Inhibitors to Human Carbonic Anhydrases I and II Authors: Srivastava, D.K. / Jude, K.M. / Banerjee, A.L. / Haldar, M. / Manokaran, S. / Kooren, J. / Mallik, S. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nmx.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nmx.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/2nmx ftp://data.pdbj.org/pub/pdb/validation_reports/nm/2nmx | HTTPS FTP |
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-Related structure data
Related structure data | 2nn1C 2nn7C 2nngC 2nnoC 2nnsC 2nnvC 2foyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28774.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P00915, carbonic anhydrase |
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-Non-polymers , 5 types, 525 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 277 K / pH: 7 Details: PEG 3350, NaCl, HEPES, Tris, pH 7.0, vapor diffusion, temperature 277K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35.45 Å / Num. obs: 78912 / % possible obs: 99.9 % / Redundancy: 6.96 % / Biso Wilson estimate: 22.53 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 6.86 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.549 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FOY Resolution: 1.55→35.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 284309.812 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.5 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→35.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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