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Open data
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Basic information
Entry | Database: PDB / ID: 1a4m | ||||||
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Title | ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 | ||||||
![]() | ADENOSINE DEAMINASE | ||||||
![]() | HYDROLASE / ADENOSINE DEAMINASE / PURINE RIBOSIDE | ||||||
Function / homology | ![]() 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 / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / 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 / adenosine metabolic process / positive regulation of T cell differentiation in thymus / AMP catabolic process / dATP catabolic process / mucus secretion / negative regulation of leukocyte migration / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / 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 / positive regulation of T cell differentiation / alpha-beta 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 calcium-mediated signaling / positive regulation of B cell proliferation / T cell activation / dendrite cytoplasm / liver development / calcium-mediated signaling / lung development / placenta development / 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 / cell adhesion / response to hypoxia / external side of plasma membrane / neuronal cell body / apoptotic process / negative regulation of apoptotic process / extracellular space / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, Z. / Quiocho, F.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.5 KB | Display | ![]() |
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PDB format | ![]() | 248.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 63.8 KB | Display | |
Data in CIF | ![]() | 91.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a4lC ![]() 2adaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PRH / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 1997 / 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: 1.95→10 Å / Num. obs: 83321 / % possible obs: 70.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.401 / % possible all: 47 |
Reflection | *PLUS Num. measured all: 415190 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 47 % / Rmerge(I) obs: 0.401 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ADA Resolution: 1.95→10 Å / Rfactor Rfree error: 0.003 / 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: 16.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 77948 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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