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- PDB-1psn: THE CRYSTAL STRUCTURE OF HUMAN PEPSIN AND ITS COMPLEX WITH PEPSTATIN -

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Basic information

Entry
Database: PDB / ID: 1psn
TitleTHE CRYSTAL STRUCTURE OF HUMAN PEPSIN AND ITS COMPLEX WITH PEPSTATIN
ComponentsPEPSIN 3A
KeywordsHYDROLASE (ACID PROTEINASE)
Function / homology
Function and homology information


multivesicular body lumen / pepsin A / Surfactant metabolism / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepsin A-5 / Pepsin A-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsFujinaga, M. / Chernaia, M.M. / Tarasova, N. / Mosimann, S.C. / James, M.N.G.
Citation
Journal: Protein Sci. / Year: 1995
Title: Crystal structure of human pepsin and its complex with pepstatin.
Authors: Fujinaga, M. / Chernaia, M.M. / Tarasova, N.I. / Mosimann, S.C. / James, M.N.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Molecular and Crystal Structures of Monoclinic Porcine Pepsin Refined at 1.8 Angstroms Resolution
Authors: Sielecki, A.R. / Fedorov, A.A. / Boodhoo, A. / Andreeva, N.S. / James, M.N.G.
History
DepositionJan 23, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPSIN 3A


Theoretical massNumber of molelcules
Total (without water)34,6321
Polymers34,6321
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.970, 151.590, 41.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 23

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Components

#1: Protein PEPSIN 3A


Mass: 34631.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00790, UniProt: P0DJD7*PLUS, pepsin A
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 60.5 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
240 %satammonium sulfate1reservoir
3100 mMNa acetate1reservoir
45 %MPD1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: SAN DIEGO MULTIWIRE DETECTION SYSTEM / Detector: AREA DETECTOR / Date: May 12, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 33057 / % possible obs: 75 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.78 Å / Num. measured all: 99655 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
GROMOSrefinement
SANDIEGO SOFTWAREdata reduction
RefinementResolution: 2.2→30 Å / σ(F): 0
Details: RESIDUES WITH ZERO OCCUPANCIES AND NEGATIVE B-FACTORS ARE DISORDERED AND THEIR POSITIONS ARE NOT CONSIDERED TO HAVE BEEN DETERMINED.
RfactorNum. reflection% reflection
Rwork0.188 --
obs-21303 89.9 %
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 0 136 2574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg2.39
X-RAY DIFFRACTIONo_improper_angle_d2.81
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg2.81

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