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- PDB-1qrp: Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-V... -

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Basic information

Entry
Database: PDB / ID: 1qrp
TitleHuman pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME
ComponentsPEPSIN 3A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE / PHOSPHONATE INHIBITOR / TRANSITION STATE ANALOGUE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
IVA VAL VAL P0L ALA MA / Chem-HH0 / Pepsin A-5 / Pepsin A-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.96 Å
AuthorsFujinaga, M. / Cherney, M.M. / Tarasova, N.I. / Bartlett, P.A. / Hanson, J.E. / James, M.N.G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.
Authors: Fujinaga, M. / Cherney, M.M. / Tarasova, N.I. / Bartlett, P.A. / Hanson, J.E. / James, M.N.
#1: 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.G.
History
DepositionJun 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: 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 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PEPSIN 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3862
Polymers34,6321
Non-polymers7541
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.900, 151.270, 40.790
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 PEPSIN 3A


Mass: 34631.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00790, UniProt: P0DJD7*PLUS
#2: Chemical ChemComp-HH0 / methyl N-[(2S)-2-({(S)-hydroxy[(1R)-3-methyl-1-{[N-(3-methylbutanoyl)-L-valyl-L-valyl]amino}butyl]phosphoryl}oxy)-3-phenylpropanoyl]-L-alanyl-L-alaninate / IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 753.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H60N5O10P / References: IVA VAL VAL P0L ALA MA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 40% AMMONIUM SULFATE, 100MM SODIUM ACETATE, 5% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlpepsin1dropin water
20.8 mMphosphonate-inhibitor1dropin ethanol
340 %satammonium sulfate1reservoir
4100 mMsodium acetate1reservoirpH5.0
55 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Aug 29, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→65 Å / Num. all: 31990 / % possible obs: 89.3 % / Observed criterion σ(F): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 1.96→2 Å / % possible all: 64.2
Reflection
*PLUS
Num. obs: 31990 / Num. measured all: 188324
Reflection shell
*PLUS
% possible obs: 64.2 %

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
XTALVIEWrefinement
GROMOS87refinement
SDMSdata scaling
RefinementResolution: 1.96→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: GROMOS87 FORCE FIELD
RfactorNum. reflection% reflection
all0.2 31976 -
obs0.2 31976 100 %
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 52 135 2625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.1
Software
*PLUS
Name: GROMOS87 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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