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Yorodumi- PDB-1w76: Orthorhombic form of Torpedo californica acetylcholinesterase (AC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w76 | ||||||
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Title | Orthorhombic form of Torpedo californica acetylcholinesterase (AChE) complexed with bis-acting galanthamine derivative | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / ALZHEIMER'S DISEASE / CHOLINESTERASE / GLYCOPROTEIN / GPI-ANCHOR / MUSCLE / NERVE / NEUROTRANSMITTER DEGRADATION / SERINE ESTERASE / SERINE HYDROLASE / SYNAPSE | ||||||
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 / OTHER / Resolution: 2.3 Å | ||||||
Authors | Greenblatt, H.M. / Guillou, C. / Guenard, D. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design. Authors: Greenblatt, H.M. / Guillou, C. / Guenard, D. / Argaman, A. / Botti, S. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L. #1: Journal: Bioorg.Med.Chem. / Year: 1998 Title: Potent Acetylcholinesterase Inhibitors: Design, Synthesis, and Structure-Activity Relationships of Bis-Interacting Ligands in the Galanthamine Series Authors: Mary, A. / Renko, D.Z. / Guillou, C. / Thal, C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w76.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w76.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 1w76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w76_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1w76_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1w76_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 1w76_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w76 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w76 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99997, -0.00714, -0.00293), Vector: |
-Components
#1: Protein | Mass: 61325.090 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-564 / Source method: isolated from a natural source Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray) Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | FIRST THREE RESIDUES IN BOTH CHAINS NOT VISIBLE. LAST 8 RESIDUES IN BOTH CHAINS NOT VISIBLE. ...FIRST THREE RESIDUES IN BOTH CHAINS NOT VISIBLE. LAST 8 RESIDUES IN BOTH CHAINS NOT VISIBLE. RESIDUES 486-489 NOT VISIBLE IN CHAIN A, BUT ARE VISIBLE IN CHAIN B. | |
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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: 3 Å3/Da / Density % sol: 59 % / Description: ISOMORPHOUS TO NATIVE ORTHORHOMBIC FORM |
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Crystal grow | Temperature: 277 K / Details: 35-40% W/V PEG 200, 0.1M MES PH5.8 4 DEG. CELSIUS |
-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 IMAGEPLATE / Detector: IMAGE PLATE / Date: Mar 19, 2001 / Details: OSMIC BLUE |
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→35 Å / Num. obs: 63928 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→34.17 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1695038.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: PHTHALIMIDE AND LINKER GROUP NOT VISIBLE FOR INHIBITORS IN EITHER ACTIVE SITE OF ASYMMETRIC UNIT. PROTEIN RESIDUES 284-289, PART OF ACTIVE SITE, HAVE LITTLE OR NO ELECTRON DENSITY IN BOTH CHAINS.
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 33.0197 Å2 / ksol: 0.3497 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.98 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→34.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.41 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
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