Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 A PYRROLIDONE-CARBOXYLATE PEPTIDASE 1 (TARGET ID NYSGRC-012831) FROM XENORHABDUS BOVIENII SS-2004 IN SPACE GROUP P21
 
Authors :  A. Ghosh, S. C. Almo, New York Structural Genomics Research Conso (Nysgrc)
Date :  24 Oct 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Nysgrc, Psi-Biology, New York Structural Genomics Research Consortium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ghosh, A. Ahmed, R. Banu, R. Bhoshle, J. Bonanno, S. Chamala, S. Chowdhury, A Fiser, A. S. Glenn, B. Hillerich, K. Khafizov, J. Lafleur, J. D. Love, R. Seidel, M. Stead, R. Toro, S. C. Almo
Crystal Structure Of A Pyrrolidone-Carboxylate Peptidase 1 (Target Id Nysgrc-012831) From Xenorhabdus Bovienii Ss-2004 In Space Group P21
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRROLIDONE-CARBOXYLATE PEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.19.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3) PRIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-206
    Gene: PCP, XBJ1_1667
    Organism Scientific: XENORHABDUS BOVIENII
    Organism Taxid: 406818
    Strain: SS-2004
    Synonym: 5-OXOPROLYL-PEPTIDASE, PYROGLUTAMYL-PEPTIDASE I

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric/Biological Unit (1, 15)
No.NameCountTypeFull Name
1CL15Ligand/IonCHLORIDE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:41 , HIS A:52BINDING SITE FOR RESIDUE CL A 301
02AC2SOFTWARELEU A:186BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREASP B:88 , ALA B:89 , ARG B:90 , PHE B:141BINDING SITE FOR RESIDUE CL B 301
04AC4SOFTWAREGLN B:70 , GLY B:72 , HOH B:477 , HOH B:509BINDING SITE FOR RESIDUE CL B 302
05AC5SOFTWAREMET B:187 , HOH B:419 , HOH D:413 , HOH D:630BINDING SITE FOR RESIDUE CL B 303
06AC6SOFTWARETHR B:185 , LEU B:186BINDING SITE FOR RESIDUE CL B 304
07AC7SOFTWAREGLN B:136 , HOH B:420BINDING SITE FOR RESIDUE CL B 305
08AC8SOFTWAREHOH B:501 , GLY C:139 , THR C:140 , CL C:303BINDING SITE FOR RESIDUE CL C 301
09AC9SOFTWARELEU C:186BINDING SITE FOR RESIDUE CL C 302
10BC1SOFTWAREASP C:88 , ARG C:90 , CL C:301BINDING SITE FOR RESIDUE CL C 303
11BC2SOFTWAREHOH A:553 , LYS D:119BINDING SITE FOR RESIDUE CL D 301
12BC3SOFTWAREHOH A:478 , GLY D:139 , THR D:140 , CL D:303BINDING SITE FOR RESIDUE CL D 302
13BC4SOFTWAREASP D:88 , ALA D:89 , ARG D:90 , CL D:302BINDING SITE FOR RESIDUE CL D 303
14BC5SOFTWAREGLY D:73 , SER D:182BINDING SITE FOR RESIDUE CL D 304
15BC6SOFTWARELEU D:186 , HOH D:550BINDING SITE FOR RESIDUE CL D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HPS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HPS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HPS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HPS)

(-) Exons   (0, 0)

(no "Exon" information available for 4HPS)

(-) 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:211
                                                                                                                                                                                                                                                   
               SCOP domains d4hpsa_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhh........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hps A  -4 LYFQSMKTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTMVNALNTAGIPASVSQTAGTFVCNHVMYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSMTLMLMTLALKIAIETAWKNTSD 206
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4hpsb_ B: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhh........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hps B  -2 FQSMKTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTMVNALNTAGIPASVSQTAGTFVCNHVMYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSMTLMLMTLALKIAIETAWKNTSD 206
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197         


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4hpsc_ C: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hps C   2 KTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTMVNALNTAGIPASVSQTAGTFVCNHVMYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSMTLMLMTLALKIAIETAWKNTSD 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     


Chain D from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4hpsd_ D: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..ee...........eee........eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhh......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hps D   2 KTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTMVNALNTAGIPASVSQTAGTFVCNHVMYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSMTLMLMTLALKIAIETAWKNTSD 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HPS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HPS)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hps)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4hps
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  D3V0W1_XENBS | D3V0W1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.19.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  D3V0W1_XENBS | D3V0W1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D3V0W1_XENBS | D3V0W1: 4gxh

(-) Related Entries Specified in the PDB File

4gxh IN SPACE GROUP P4322 RELATED ID: NYSGRC-012831 RELATED DB: TARGETTRACK