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Yorodumi- PDB-1zgb: Crystal Structure of Torpedo Californica Acetylcholinesterase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zgb | ||||||
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Title | Crystal Structure of Torpedo Californica Acetylcholinesterase in Complex With an (R)-Tacrine(10)-Hupyridone Inhibitor. | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / SERINE-HYDROLASE / PROTEIN-INHIBITOR COMPLEX / ENANTIOMERIC SELECTIVITY / Israel Structural Proteomics Center / ISPC / Structural Genomics | ||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Torpedo californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Haviv, H. / Wong, D.M. / Greenblatt, H.M. / Carlier, P.R. / Pang, Y.P. / Silman, I. / Sussman, J.L. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Crystal Packing Mediates Enantioselective Ligand Recognition at the Peripheral Site of Acetylcholinesterase Authors: Haviv, H. / Wong, D.M. / Greenblatt, H.M. / Carlier, P.R. / Pang, Y.P. / Silman, I. / Sussman, J.L. #1: Journal: BIOORG.MED.CHEM.LETT. / Year: 1999 Title: Potent, easily synthesized huperzine A-tacrine hybrid acetylcholinesterase inhibitors Authors: Carlier, P.R. / Du, D.-M. / Han, Y.-F. / Liu, J. / Pang, Y.-P. #2: Journal: J.Am.Chem.Soc. / Year: 2003 Title: Acetylcholinesterase Complexed with Bivalent Ligands Related to Huperzine A: Experimental Evidence for Species-Dependent Protein-Ligand Complementarity Authors: Wong, D.M. / Greenblatt, H.M. / Dvir, H. / Carlier, P.R. / Han, Y.-F. / Pang, Y.-P. / Silman, I. / Sussman, J.L. #3: Journal: NAT.STRUCT.BIOL. / Year: 1997 Title: Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A Authors: Raves, M.L. / Harel, M. / Pang, Y.-P. / Silman, I. / Kozikowski, A.P. / Sussman, J.L. #4: Journal: Science / Year: 1991 Title: Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zgb.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zgb.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zgb_validation.pdf.gz | 676.6 KB | Display | wwPDB validaton report |
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Full document | 1zgb_full_validation.pdf.gz | 686.8 KB | Display | |
Data in XML | 1zgb_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 1zgb_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgb ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Torpedo californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase | ||||||
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#2: Sugar | #3: Chemical | ChemComp-A1E / ( | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.7 % |
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Crystal grow | Temperature: 277 K Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP. PROTEIN WAS CRYSTALLISED FROM 28% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, SEEDING WITH TRIGONAL MICROCRYSTALS; THEN SOAKED IN ...Details: PEG 200, pH 5.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP. PROTEIN WAS CRYSTALLISED FROM 28% V/V PEG 200 0.5 M MES PH 5.8 AT 277K, SEEDING WITH TRIGONAL MICROCRYSTALS; THEN SOAKED IN MOTHER LIQUOR (40% V/V PEG 200 IN 0.1 M MES BUFFER, PH 5.8) CONTAINING 2 MM (RS)-(+/-)- TACRINE(10)-HUPYRIDONE ((5RS)-(+/-)-5-{[10-(1,2,3,4-TETRAHYDROACRIDIN-9-YLAMINO) DECYL] AMINO}-5,6,7,8-TETRAHYDRO-QUINOLIN-2(1H)-ONE) BIS-OXALATE FOR 17 HOURS. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2000 / Details: OSMIC BLUE CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 44250 / % possible obs: 98.5 % / Redundancy: 1.59 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.16 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.19 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1962219.64 / 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: 35.49 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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