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- PDB-6pad: Binding of chloromethyl ketone substrate analogues to crystalline... -

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Basic information

Entry
Database: PDB / ID: 6pad
TitleBinding of chloromethyl ketone substrate analogues to crystalline papain
ComponentsPAPAIN
KeywordsHYDROLASE/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
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
BENZYLOXYCARBONYL-PHENYLALANYL-METHYLENYLALANYL / Chem-0PC / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsDrenth, 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.
History
DepositionNov 1, 1976Processing site: BNL
SupersessionApr 12, 1977ID: 7PAP
Revision 1.0Apr 12, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8522
Polymers23,4491
Non-polymers4031
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.000, 104.300, 50.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 152 IS A CIS PROLINE.
2: SOME COORDINATES WERE AFFECTED BY THE BINDING OF THE INHIBITOR.

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Components

#1: Protein PAPAIN


Mass: 23449.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Tissue: FRUIT LATEX / References: UniProt: P00784, papain
#2: Chemical ChemComp-0PC / Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro-1-methyl-2-oxopropyl]-L-phenylalaninamide / ZPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 402.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN2O4 / References: BENZYLOXYCARBONYL-PHENYLALANYL-METHYLENYLALANYL
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
167 %(v/v)methanol1drop
230 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.8 Å

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Processing

RefinementHighest resolution: 2.8 Å
Details: 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 ...Details: 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. THE COORDINATES OF THE INHIBITOR WERE NOT REFINED.
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 27 30 1712

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