+Open data
-Basic information
Entry | Database: PDB / ID: 1khp | ||||||
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Title | Monoclinic form of papain/ZLFG-DAM covalent complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE INHIBITOR / DIAZOMETHYLKETONE INHIBITOR / IRREVERSIBLE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Jaskolski, M. | ||||||
Citation | Journal: J.Pept.Res. / Year: 2004 Title: Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor Authors: Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Jaskolski, M. #1: Journal: ACTA BIOCHIM.POL. / Year: 1997 Title: Crystallization and preliminary crystallographic studies of a new crystal form of papain from Carica papaya. Authors: Kozak, M. / Kozian, E. / Grzonka, Z. / Jaskolski, M. #2: Journal: ACTA BIOCHIM.POL. / Year: 2001 Title: Structural studies of cysteine proteases and their inhibitors Authors: Grzonka, Z. / Jankowska, E. / Wieczerzak, E. / Kasprzykowski, F. / Lankiewicz, L. / Wiczk, W. / Drabik, P. / Ciarkowski, J. / Janowski, R. / Kozak, M. / Jaskolski, M. / Grubb, A. #3: Journal: Biochemistry / Year: 1976 Title: Binding of chloromethyl ketone substrate analogues to crystalline papain. Authors: Drenth, J. / Kalk, K.H. / Swen, H.M. #4: Journal: ACTA CRYSTALLOGR.,SECT.B / Year: 1992 Title: Structure of monoclinic papain at 1.60 Angstroms resolution. Authors: Pickersgill, R.W. / Harris, G.W. / Garman, E. #5: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1999 Title: Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity? Authors: Czaplewski, C. / Grzonka, Z. / Jaskolski, M. / Kasprzykowski, F. / Kozak, M. / Politowska, E. / Ciarkowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1khp.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1khp.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 1khp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1khp_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 1khp_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 1khp_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1khp_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1khp ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1khp | HTTPS FTP |
-Related structure data
Related structure data | 1khqC 1ppnS 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
#1: Protein | Mass: 23452.301 Da / Num. of mol.: 1 / Fragment: Papain, Residues 134-345 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: P00784, papain |
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#2: Protein/peptide | |
#3: Water | ChemComp-HOH / |
Compound details | THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...THE PEPTIDIC INHIBITOR IS COVALENTLY |
Nonpolymer details | THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...THE PEPTIDIC INHIBITOR IS COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 68% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 292 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 12041 / Num. obs: 12041 / % possible obs: 88.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2 / % possible all: 75.1 |
Reflection | *PLUS Num. measured all: 57694 |
Reflection shell | *PLUS % possible obs: 75.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPN Resolution: 2→10 Å / SU B: 6.19632 / SU ML: 0.16795 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2612 / ESU R Free: 0.19839 / Stereochemistry target values: Engh & Huber Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. THE PHQ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE ...Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. THE PHQ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE TO DISORDER AND WAS NOT INCLUDED IN THE MODEL.
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Displacement parameters | Biso mean: 22.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |