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- PDB-1stf: THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT ... -

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Basic information

Entry
Database: PDB / ID: 1stf
TitleTHE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION
Components
  • PAPAIN
  • STEFIN B (CYSTATIN B)
KeywordsHYDROLASE(SULFHYDRYL PROTEINASE)
Function / homology
Function and homology information


negative regulation of peptidase activity / papain / endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity / serpin family protein binding / negative regulation of proteolysis / cysteine-type peptidase activity / adult locomotory behavior / tertiary granule lumen / protease binding ...negative regulation of peptidase activity / papain / endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity / serpin family protein binding / negative regulation of proteolysis / cysteine-type peptidase activity / adult locomotory behavior / tertiary granule lumen / protease binding / : / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / nucleolus / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesCarica papaya (papaya)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.37 Å
AuthorsStubbs, M.T. / Laber, B. / Bode, W.
Citation
Journal: EMBO J. / Year: 1990
Title: The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction.
Authors: Stubbs, M.T. / Laber, B. / Bode, W. / Huber, R. / Jerala, R. / Lenarcic, B. / Turk, V.
#1: Journal: FEBS Lett. / Year: 1991
Title: Minireview: The Cystatins: Protein Inhibitors of Cysteine Proteinases
Authors: Turk, V. / Bode, W.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1990
Title: Mutations in the Qvvag Region of the Cysteine Proteinase Inhibitor Stefin B
Authors: Jerala, R. / Trstenjak-Prebanda, M. / Kroon-Zitko, L. / Lenarcic, B. / Turk, V.
History
DepositionApr 21, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PAPAIN
I: STEFIN B (CYSTATIN B)


Theoretical massNumber of molelcules
Total (without water)34,6812
Polymers34,6812
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-12 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 67.000, 169.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO E 152
2: VAL I 66 - GLY I 67 OMEGA =214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein PAPAIN


Mass: 23507.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P00784, papain
#2: Protein STEFIN B (CYSTATIN B)


Mass: 11173.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P04080
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG15501reservoir
20.75 Mphosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.37 Å / Num. obs: 16084 / % possible obs: 89 % / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 2.44 Å

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.37→8 Å /
RfactorNum. reflection
Rwork0.19 -
obs-16033
Refinement stepCycle: LAST / Resolution: 2.37→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 4 142 2590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.1
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 8 Å / Num. reflection obs: 16033 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.1

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