+Open data
-Basic information
Entry | Database: PDB / ID: 3aig | |||||||||
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Title | ADAMALYSIN II WITH PEPTIDOMIMETIC INHIBITOR POL656 | |||||||||
Components | ADAMALYSIN II | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SNAKE VENOM METALLOENDOPETIDASE / ZINC PROTEASE / METALLOPROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information adamalysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Crotalus adamanteus (eastern diamondback rattlesnake) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å | |||||||||
Authors | Gomis-Rueth, F.X. / Meyer, E.F. / Kress, L.F. / Politi, V. | |||||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Structures of adamalysin II with peptidic inhibitors. Implications for the design of tumor necrosis factor alpha convertase inhibitors. Authors: Gomis-Ruth, F.X. / Meyer, E.F. / Kress, L.F. / Politi, V. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with ...Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with Astacin, Collagenase and Thermolysin Authors: Gomis-Ruth, F.X. / Kress, L.F. / Kellermann, J. / Mayr, I. / Lee, X. / Huber, R. / Bode, W. #2: Journal: Embo J. / Year: 1993 Title: First Structure of a Snake Venom Metalloproteinase: A Prototype for Matrix Metalloproteinases/Collagenases Authors: Gomis-Ruth, F.X. / Kress, L.F. / Bode, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aig.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aig.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 3aig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aig_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 3aig_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 3aig_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 3aig_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3aig ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3aig | HTTPS FTP |
-Related structure data
Related structure data | 2aigC 1iagS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23152.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Crotalus adamanteus (eastern diamondback rattlesnake) Secretion: VENOM References: GenBank: 547144, UniProt: P34179*PLUS, adamalysin |
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-Non-polymers , 5 types, 133 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-0ZC / ( |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THE SEQUENCE USED IN THIS ENTRY WAS DETERMINEDSource details | THE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION TO RENDER ...THE N-TERMINUS WAS BLOCKED AGAINST AMINOPEPTI | |
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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: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Details: 1.8 M AMMONIUM SULFATE |
Crystal grow | *PLUS pH: 5 / Method: unknown / Details: Gomis-Ruth, F.X., (1993) Embo J., 12, 4151. |
Components of the solutions | *PLUS Conc.: 1.8 M / Common name: ammonium sulfate |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Monochromator: NI-FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 8311 / % possible obs: 78.9 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.5→2.63 Å / % possible all: 45.7 |
Reflection | *PLUS Num. measured all: 18531 |
Reflection shell | *PLUS % possible obs: 45.7 % / Redundancy: 1.7 % / Num. unique obs: 680 / Num. measured obs: 1153 / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: NATIVE ADAMALYSIN II (PDB ENTRY 1IAG) Resolution: 2.8→7 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.8→7 Å
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Refine LS restraints |
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