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- PDB-3pep: REVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A... -

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Basic information

Entry
Database: PDB / ID: 3pep
TitleREVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A FLEXIBLE SUBDOMAIN
ComponentsPEPSIN
KeywordsHYDROLASE (ACID PROTEINASE)
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
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsAbad-Zapatero, C. / Erickson, J.W.
CitationJournal: Proteins / Year: 1990
Title: Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain
Authors: Abad-Zapatero, C. / Rydel, T.J. / Erickson, J.
History
DepositionOct 24, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET VI CORRESPONDS TO SHEET C2 (POSSIBLY FOR PSI2) OF PROTEIN DATA BANK ENTRY *2APR* ...SHEET SHEET VI CORRESPONDS TO SHEET C2 (POSSIBLY FOR PSI2) OF PROTEIN DATA BANK ENTRY *2APR* (RHIZOPUSPEPSIN, A SIMILAR ASPARTYL PROTEINASE). IN PEPSIN THIS SHEET HAS ONE MORE STRAND. THE EXTENDED SHEET VII CORRESPONDS TO SHEETS C1 (POSSIBLY BECAUSE OF PSI1) AND BIFURCATED SHEET 4A OF *2APR**. THE EXTENDED SHEET DESCRIPTION WAS USED IN THIS ENTRY BECAUSE THERE ARE THREE GOOD HYDROGEN BONDS BETWEEN STRANDS 3 AND 4. THE OVERALL STRUCTURE IS WELL CONSERVED BETWEEN THE TWO ENZYMES AS WELL AS AMONG OTHER FUNGAL PROTEINASES (PENNICILLOPEPSIN AND ENDOTHIAPEPSIN).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6073
Polymers34,5141
Non-polymers922
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.270, 73.820, 36.440
Angle α, β, γ (deg.)90.00, 90.00, 103.38
Int Tables number4
Space group name H-MP1121
Atom site foot note1: THE ELECTRON DENSITY FOR RESIDUES 292 - 296 IS WEAK IN THE FINAL MAP, INDICATING HIGH MOBILITY AND/OR DISORDER. THE CONFORMATION FOR THESE RESIDUES SHOULD BE CONSIDERED AS TENTATIVE. THE ELECTRON ...1: THE ELECTRON DENSITY FOR RESIDUES 292 - 296 IS WEAK IN THE FINAL MAP, INDICATING HIGH MOBILITY AND/OR DISORDER. THE CONFORMATION FOR THESE RESIDUES SHOULD BE CONSIDERED AS TENTATIVE. THE ELECTRON DENSITY IS ALSO WEAK FOR RESIDUES IN THE TURN ASP 278 - SER 281.
2: RESIDUE PRO 23 IS A CIS PROLINE.

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Components

#1: Protein PEPSIN


Mass: 34514.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791, pepsin A
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal grow
*PLUS
pH: 2 / Method: unknown
Details: Andreeva, N.S. et al (1984). J. Biol. Chem., 259, 11353-11365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %enzyme11
220 %ethanol11
32.5 Msulfuric acid11

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 5 Å / Num. obs: 8742 / % possible obs: 77 % / Rmerge(I) obs: 0.145

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→5 Å
Details: THE DENSITY FOR HOH 757 IS ELONGATED AND ITS SHAPE COULD VERY WELL CORRESPOND TO AN ETHANOL MOLECULE (EOH 901). THE SAME IS TRUE FOR HOH 694 (EOH 902). THUS THIS ENTRY CONTAINS TENTATIVE ...Details: THE DENSITY FOR HOH 757 IS ELONGATED AND ITS SHAPE COULD VERY WELL CORRESPOND TO AN ETHANOL MOLECULE (EOH 901). THE SAME IS TRUE FOR HOH 694 (EOH 902). THUS THIS ENTRY CONTAINS TENTATIVE COORDINATES FOR TWO WELL-DEFINED ETHANOL MOLECULES IN THE VICINITY OF THE ACTIVE SITE (CORRESPONDING TO THESE TWO WATER MOLECULES). A THIRD, WEAKER, ETHANOL COULD BE HYDROGEN BONDED TO ASP 32 BUT THE DENSITY IS NOT UNEQUIVOCAL. THIS ETHANOL WOULD COMPRISE WATERS 452, 752, AND 756. APPROXIMATELY 10 PER CENT OF THE SOLVENT MOLECULES ARE PROBABLY ETHANOL MOLECULES. THE SPACE GROUP SETTING USED IN THIS ANALYSIS IS THE FIRST SETTING FOR MONOCLINIC SPACE GROUPS, WITH THE Z AXIS AS THE UNIQUE AXIS. FOR DETAILS PLEASE CONSULT THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY. THE ELECTRON DENSITY FOR RESIDUES 292 - 296 IS WEAK IN THE FINAL MAP, INDICATING HIGH MOBILITY AND/OR DISORDER. THE CONFORMATION FOR THESE RESIDUES SHOULD BE CONSIDERED AS TENTATIVE. THE ELECTRON DENSITY IS ALSO WEAK FOR RESIDUES IN THE TURN ASP 278 - SER 281.
RfactorNum. reflection
obs0.171 8742
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 0 212 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0640.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.41
X-RAY DIFFRACTIONp_mcangle_it3.91.5
X-RAY DIFFRACTIONp_scbond_it2.81.5
X-RAY DIFFRACTIONp_scangle_it4.22
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1650.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1060.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.53
X-RAY DIFFRACTIONp_staggered_tor19.215
X-RAY DIFFRACTIONp_orthonormal_tor19.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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