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- PDB-1psa: STRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOV... -

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Basic information

Entry
Database: PDB / ID: 1psa
TitleSTRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOVEL CRYSTAL PACKING INDUCED BY MINOR CHEMICAL ALTERATIONS IN THE INHIBITOR
ComponentsPEPSIN A
KeywordsHYDROLASE/hydrolase inhibitor / ACID PROTEINASE / HYDROLASE-hydrolase inhibitor complex
Function / homology
Function and homology information


Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular region
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
N-(ethoxycarbonyl)-L-leucyl-N-[(1R,2S,3S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methylhexyl]-L-leucinamide / Chem-0ZL / Pepsin A
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsChen, L. / Abad-Zapatero, C.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure of a pepsin/renin inhibitor complex reveals a novel crystal packing induced by minor chemical alterations in the inhibitor.
Authors: Chen, L. / Erickson, J.W. / Rydel, T.J. / Park, C.H. / Neidhart, D. / Luly, J. / Abad-Zapatero, C.
#1: Journal: Adv.Exp.Med.Biol. / Year: 1991
Title: Inhibitor Binding Induces Structural Changes in Porcine Pepsin
Authors: Abad-Zapatero, C. / Rydel, T.J. / Neidhart, D.J. / Luly, J. / Erickson, J.W.
#2: Journal: Proteins / Year: 1990
Title: Revised 2.3 Angstroms Structure of Porcine Pepsin: Evidence for a Flexible Subdomain
Authors: Abad-Zapatero, C. / Rydel, T.J. / Erickson, J.
History
DepositionOct 22, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Nov 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 1.5Oct 30, 2024Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _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
A: PEPSIN A
B: PEPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1114
Polymers69,0272
Non-polymers1,0842
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.100, 74.400, 76.500
Angle α, β, γ (deg.)90.00, 90.00, 100.80
Int Tables number4
Space group name H-MP1121
Atom site foot note1: RESIDUES PRO A 23 AND PRO B 23 ARE CIS PROLINES.
2: RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* HAD THE WEAKEST ELECTRON DENSITY.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.786, 0.036, 0.617), (0.043, -0.993, 0.113), (0.616, 0.116, 0.779)
Vector: 54.298, 43.481, -21.646)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein PEPSIN A


Mass: 34513.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791, pepsin A
#2: Chemical ChemComp-0ZL / N-(ethoxycarbonyl)-L-leucyl-N-[(1R,2S,3S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methylhexyl]-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 541.763 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H55N3O6
References: N-(ethoxycarbonyl)-L-leucyl-N-[(1R,2S,3S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methylhexyl]-L-leucinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR A-62095 IS A TETRAPEPTIDE ANALOGUE WITH A T-BOC BLOCKING GROUP AND CONTAINING ...THE INHIBITOR A-62095 IS A TETRAPEPTIDE ANALOGUE WITH A T-BOC BLOCKING GROUP AND CONTAINING CYCLOHEXYL ALANINE AT THE P1 POSITION (XAO).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal grow
*PLUS
pH: 2 / Method: unknown
Details: taken from Andreeva, N.S. et al (1984). J. Biol. Chem., 259, 11353-11365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme11
220 %ethanol11
32.5 Msulfuric acid11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Num. all: 13736 / Num. obs: 11951 / % possible obs: 87 % / Num. measured all: 24379 / Rmerge(I) obs: 0.044

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.9→8 Å / Rfactor Rwork: 0.139
Details: THE SPACE GROUP OF THIS STRUCTURE IS MONOCLINIC P21, WITH C AXIS UNIQUE. THE ASYMMETRIC UNIT CONTAINS TWO PEPSIN/ INHIBITOR COMPLEXES. RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* ...Details: THE SPACE GROUP OF THIS STRUCTURE IS MONOCLINIC P21, WITH C AXIS UNIQUE. THE ASYMMETRIC UNIT CONTAINS TWO PEPSIN/ INHIBITOR COMPLEXES. RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* HAD THE WEAKEST ELECTRON DENSITY.
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 76 110 5044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg3.17
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection all: 11284 / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.17
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_improper_angle_d1.3

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