Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE ALPHA-LYTIC PROTEASE AT 1.6 A, PH 5.14
 
Authors :  A. I. Derman, T. Mau, D. A. Agard
Date :  16 Jun 99  (Deposition) - 18 Jun 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Folding, Pro Region, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. I. Derman, T. Mau, D. A. Agard
A Genetic Screen That Targets Specifically The Folding Transition State Of Alpha-Lytic Protease
To Be Published 1999
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-LYTIC PROTEASE
    ChainsA
    EC Number3.4.21.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPALP12
    Expression System Taxid562
    Expression System VectorPLASMID
    FragmentMATURE PROTEASE DOMAIN, RESIDUES 1-198
    Organism ScientificLYSOBACTER ENZYMOGENES
    Organism Taxid69

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , ARG A:78 , GLN A:190 , TYR A:191 , HOH A:230 , HOH A:231 , HOH A:232 , HOH A:380 , HOH A:381 , HOH A:382 , HOH A:429BINDING SITE FOR RESIDUE SO4 A 202
2AC2SOFTWAREALA A:1 , ASN A:2 , ARG A:183 , PRO A:186 , HOH A:207 , HOH A:273 , HOH A:342 , HOH A:343 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE SO4 A 203
3AC3SOFTWAREHIS A:36 , ARG A:89 , ARG A:140 , GLY A:141 , SER A:143 , GOL A:201 , HOH A:361 , HOH A:362 , HOH A:363BINDING SITE FOR RESIDUE SO4 A 204
4AC4SOFTWAREHIS A:36 , ARG A:89 , TYR A:123 , GLU A:125 , SER A:159 , GLY A:160 , SO4 A:204BINDING SITE FOR RESIDUE GOL A 201

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:17 -A:37
2A:101 -A:111
3A:137 -A:170

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QRX)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.PRLA_LYSEN231-236  1A:32-37
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.PRLA_LYSEN336-347  1A:137-148

(-) Exons   (0, 0)

(no "Exon" information available for 1QRX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
           PRLA_LYSEN   200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 397
               SCOP domains d1qrxa_ A: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --1qrxA01 A:3-76,A:184-196 Trypsin-like serine proteases                    1qrxA02 A:77-183 Trypsin-like serine proteases                                                             1qrxA01      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...eeee..eeeee..eeeeeehhhhh....eeee..eeeeeeeeee.....eeeeee....eeeeeeee..eeee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee.....eeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qrx A   1 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QRX)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRLA_LYSEN | P00778)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:59 - Pro A:60   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qrx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRLA_LYSEN | P00778
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.12
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PRLA_LYSEN | P00778
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PRLA_LYSEN | P007781boq 1gba 1gbb 1gbc 1gbd 1gbe 1gbf 1gbh 1gbi 1gbj 1gbk 1gbl 1gbm 1p01 1p02 1p03 1p04 1p05 1p06 1p09 1p10 1p11 1p12 1qq4 1qrw 1ssx 1tal 2alp 2h5c 2h5d 2lpr 2pro 2ull 3lpr 3m7t 3m7u 3pro 3qgj 3urc 3urd 3ure 4pro 5lpr 6lpr 7lpr 8lpr 9lpr

(-) Related Entries Specified in the PDB File

1qq4 THE STRUCTURE OF THE R102H/G134S MUTANT AT THE SAME PH (5.14).
1tal THE TRUCTURE OF SAME MOLECULE DETERMINED AT PH 8. IN ADDITION, THE TRIS MOLECULE (TAM) IN 1TAL SHOULD HAVE BEEN MODELED AS A GLYCEROL MOLECULE, AS IT IS DONE IN THIS ENTRY.