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- PDB-1khq: ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1khq
TitleORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX
Components
  • Papain
  • peptidic inhibitor
KeywordsHYDROLASE/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
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJanowski, 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
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id
Remark 600HETEROGEN THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...HETEROGEN THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP OF THE HETGROUP GLM (-N-CH2-CO-CH2-). THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL- (Z- OR CBZ-) GROUP (NOT VISIBLE IN ELECTRON DENSITY).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Papain
I: peptidic inhibitor


Theoretical massNumber of molelcules
Total (without water)23,9642
Polymers23,9642
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.89, 96.74, 49.88
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Papain / Papaya proteinase I / PPI


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
#2: Protein/peptide peptidic inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 512.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP. THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-GROUP PHQ WHICH IS NOT VISIBLE IN ELECTRON DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 72% 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
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
134 mM1reservoirNaCl
250 mM2-aminoethanol-HCl1reservoirpH9.2
330 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 22, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 26000 / Num. obs: 26000 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.7
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / % possible all: 89.6
Reflection
*PLUS
Num. measured all: 211148
Reflection shell
*PLUS
Highest resolution: 1.63 Å / % possible obs: 89.6 % / Rmerge(I) obs: 0.29

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPN

1ppn


Resolution: 1.6→10 Å / SU B: 1.91608 / SU ML: 0.06724 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07936 / ESU R Free: 0.07645 / Stereochemistry target values: Engh & Huber
Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. PARAMETERS WERE USED. THE CBZ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE ...Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. PARAMETERS WERE USED. THE CBZ (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.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 1304 5 %RANDOM
Rwork0.147 ---
all0.149 24603 --
obs0.149 24603 95.1 %-
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 0 105 1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.021
X-RAY DIFFRACTIONp_angle_d0.0240.03
X-RAY DIFFRACTIONp_angle_deg1.564
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9181.5
X-RAY DIFFRACTIONp_mcangle_it1.6262
X-RAY DIFFRACTIONp_scbond_it2.7073
X-RAY DIFFRACTIONp_scangle_it4.4324.5
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.1040.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor Rwork: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS

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