[English] 日本語
Yorodumi- PDB-2pad: BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO CRYSTALLINE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pad | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO CRYSTALLINE PAPAIN | ||||||||||||
Components | PAPAIN | ||||||||||||
Keywords | HYDROLASE (SULFHYDRYL PROTEINASE) | ||||||||||||
Function / homology | Function and homology information papain / serpin family protein binding / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||||||||
Biological species | Carica papaya (papaya) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||||||||
Authors | Drenth, J. / Kalk, K.H. / Swen, H.M. | ||||||||||||
Citation | Journal: Biochemistry / Year: 1976 Title: Binding of chloromethyl ketone substrate analogues to crystalline papain. Authors: Drenth, J. / Kalk, K.H. / Swen, H.M. #1: Journal: Adv.Protein Chem. / Year: 1971 Title: The Structure of Papain Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Wolthers, B.G. #2: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1970 Title: The Structure of the Papain Molecule Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Sluyterman, L.A.A. / Wolthers, B.G. #3: Journal: Nature / Year: 1968 Title: Structure of Papain Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Swen, H.M. / Wolthers, B.G. | ||||||||||||
History |
| ||||||||||||
Remark 700 | SHEET THE SHEET SUBSTRUCTURE OF THIS MOLECULE IS DOUBLY BIFURCATED. IN ORDER TO REPRESENT THIS ...SHEET THE SHEET SUBSTRUCTURE OF THIS MOLECULE IS DOUBLY BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 4,5,6 OF S1A ARE IDENTICAL TO STRANDS 2,3,4 OF S1B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pad.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pad.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pad_validation.pdf.gz | 386.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2pad_full_validation.pdf.gz | 417.4 KB | Display | |
Data in XML | 2pad_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2pad_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pad ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pad | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUE 152 IS A CIS PROLINE. 2: SOME COORDINATES WERE AFFECTED BY THE BINDING OF THE INHIBITOR. |
-Components
#1: Protein | Mass: 23449.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carica papaya (papaya) / References: UniProt: P00784, papain |
---|---|
#2: Chemical | ChemComp-CYS / |
#3: Water | ChemComp-HOH / |
Compound details | IN THIS STRUCTURE THE ENZYME IS IRREVERSIBLY INHIBITED BY A CYSTEINE MOLECULE DISULFIDE BOUND TO ...IN THIS STRUCTURE THE ENZYME IS IRREVERSIB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
|
-Processing
Refinement | Highest resolution: 2.8 Å | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
|