+Open data
-Basic information
Entry | Database: PDB / ID: 1a4l | ||||||
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Title | ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0 | ||||||
Components | ADENOSINE DEAMINASE | ||||||
Keywords | HYDROLASE / ADENOSINE DEAMINASE / PENTOSTATIN / DEOXYCOFORMYCIN | ||||||
Function / homology | Function and homology information mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / histamine secretion / cytoplasmic vesicle lumen / inosine biosynthetic process / 2'-deoxyadenosine deaminase activity / amide catabolic process / adenosine deaminase / hypoxanthine biosynthetic process / germinal center B cell differentiation / adenosine catabolic process / adenosine deaminase activity / inhibition of non-skeletal tissue mineralization / hypoxanthine salvage / deoxyadenosine catabolic process / dAMP catabolic process / AMP catabolic process / adenosine metabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / mucus secretion / negative regulation of leukocyte migration / regulation of cell-cell adhesion mediated by integrin / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / response to purine-containing compound / GMP salvage / IMP salvage / positive regulation of smooth muscle contraction / Peyer's patch development / germinal center formation / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / negative regulation of thymocyte apoptotic process / anchoring junction / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / positive regulation of heart rate / leukocyte migration / lung alveolus development / positive regulation of T cell receptor signaling pathway / thymocyte apoptotic process / B cell proliferation / T cell differentiation / smooth muscle contraction / : / response to vitamin E / positive regulation of B cell proliferation / T cell activation / positive regulation of calcium-mediated signaling / dendrite cytoplasm / lung development / liver development / placenta development / calcium-mediated signaling / negative regulation of inflammatory response / positive regulation of T cell activation / T cell receptor signaling pathway / T cell differentiation in thymus / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / neuronal cell body / negative regulation of apoptotic process / apoptotic process / extracellular space / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wang, Z. / Quiocho, F.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. Authors: Wang, Z. / Quiocho, F.A. #1: Journal: Biochemistry / Year: 1993 Title: A Pre-Transition-State Mimic of an Enzyme: X-Ray Structure of Adenosine Deaminase with Bound 1-Deazaadenosine and Zinc-Activated Water Authors: Wilson, D.K. / Quiocho, F.A. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Refined 2.5 A Structure of Murine Adenosine Deaminase at Ph 6.0 Authors: Sharff, A.J. / Wilson, D.K. / Chang, Z. / Quiocho, F.A. #3: Journal: Science / Year: 1991 Title: Atomic Structure of Adenosine Deaminase Complexed with a Transition-State Analog: Understanding Catalysis and Immunodeficiency Mutations Authors: Wilson, D.K. / Rudolph, F.B. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4l.cif.gz | 289.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4l.ent.gz | 230.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a4l_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1a4l_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1a4l_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 1a4l_validation.cif.gz | 71.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4l ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4l | HTTPS FTP |
-Related structure data
Related structure data | 1a4mC 2adaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39715.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): PRC4 / References: UniProt: P03958, adenosine deaminase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-DCF / #4: 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: 2.6 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→10 Å / Num. obs: 47806 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.095 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.249 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 330776 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ADA Resolution: 2.6→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 13.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 43502 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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