[English] 日本語
Yorodumi- PDB-4pad: Binding of chloromethyl ketone substrate analogues to crystalline... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pad | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Binding of chloromethyl ketone substrate analogues to crystalline papain | ||||||||||||
Components | PAPAIN | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SULFHYDRYL PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis Similarity search - Function | ||||||||||||
Biological species | Carica papaya (papaya) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||||||||
Authors | Drenth, J. | ||||||||||||
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 | 4pad.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pad.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pad ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pad | 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-TCK / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.01 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-Processing
Refinement | Highest resolution: 2.8 Å Details: THE COORDINATES OF THE INHIBITOR WERE NOT REFINED. THIS DATA SET WAS OBTAINED BY MERGING THE INHIBITOR COORDINATES WITH THE REFINED NATIVE PAPAIN COORDINATES OF SET 8PAP. THE CONFORMATION OF ...Details: THE COORDINATES OF THE INHIBITOR WERE NOT REFINED. THIS DATA SET WAS OBTAINED BY MERGING THE INHIBITOR COORDINATES WITH THE REFINED NATIVE PAPAIN COORDINATES OF SET 8PAP. THE CONFORMATION OF RESIDUE CYS 25 IN THIS DERIVATIVE STRUCTURE IS NOT THE SAME AS THAT IN THE NATIVE ENZYME AND THIS FACT IS REFLECTED IN THE COORDINATES | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
|