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(-) Description

Title :  CRYSTAL STRUCTURE OF A PYRROLIDONE-CARBOXYLATE PEPTIDASE 1 (TARGET ID NYSGRC-012831) FROM XENORHABDUS BOVIENII SS-2004
 
Authors :  A. Ghosh, S. C. Almo, New York Structural Genomics Research Conso (Nysgrc)
Date :  04 Sep 12  (Deposition) - 19 Sep 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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, R. Bhoshle, R. Toro, A. Gizzi, B. Hillerich, R. Seidel, S. C. Almo, New York Structural Genomics Research Consortium
Crystal Structure Of A Pyrrolidone-Carboxylate Peptidase 1 (Target Id Nysgrc-012831) From Xenorhabdus Bovienii Ss-2004 (Casp Target)
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
    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  (3, 30)

Asymmetric/Biological Unit (3, 30)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MSE21Mod. Amino AcidSELENOMETHIONINE
3PO45Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:117 , ILE A:118 , LYS A:119 , THR A:120BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREPHE A:12 , ASN A:18 , GLY A:69 , GLN A:70BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWAREPRO B:117 , ILE B:118 , LYS B:119 , THR B:120 , SER B:205BINDING SITE FOR RESIDUE PO4 B 301
4AC4SOFTWAREASN B:18 , GLN B:70BINDING SITE FOR RESIDUE CL B 302
5AC5SOFTWAREPRO C:117 , ILE C:118 , LYS C:119 , THR C:120BINDING SITE FOR RESIDUE PO4 C 301
6AC6SOFTWAREASN C:18 , GLN C:70BINDING SITE FOR RESIDUE CL C 302
7AC7SOFTWARELEU D:171 , PRO D:172 , THR D:185 , LEU D:186BINDING SITE FOR RESIDUE PO4 D 301
8AC8SOFTWAREPRO D:117 , ILE D:118 , LYS D:119 , THR D:120BINDING SITE FOR RESIDUE PO4 D 302
9AC9SOFTWAREASN D:18 , GLN D:70BINDING SITE FOR RESIDUE CL D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GXH)

(-) 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:202
                                                                                                                                                                                                                                          
               SCOP domains d4gxha_ A: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..........................eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxh A   2 KTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTmVNALNTAGIPASVSQTAGTFVCNHVmYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSmTLmLmTLALKIAIETAWKN 203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181  |  | 191       201  
                                                                                                                                                 121-MSE                   147-MSE                              184-MSE|              
                                                                                                                                                                                                                   187-MSE            
                                                                                                                                                                                                                     189-MSE          


Chain B from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4gxhb_ 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..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxh B   1 mKTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTmVNALNTAGIPASVSQTAGTFVCNHVmYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSmTLmLmTLALKIAIETAWKNTS 205
                            |       10        20        30        40        50        60        70        80        90       100       110       120|      130       140      |150       160       170       180   |  |190       200     
                            1-MSE                                                                                                                 121-MSE                   147-MSE                              184-MSE|                
                                                                                                                                                                                                                    187-MSE              
                                                                                                                                                                                                                      189-MSE            


Chain C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains d4gxhc_ C: 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
                 4gxh C   2 KTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTmVNALNTAGIPASVSQTAGTFVCNHVmYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSmTLmLmTLALKIAIETAWKN 203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181  |  | 191       201  
                                                                                                                                                 121-MSE                   147-MSE                              184-MSE|              
                                                                                                                                                                                                                   187-MSE            
                                                                                                                                                                                                                     189-MSE          


Chain D from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains d4gxhd_ 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
                 4gxh D   2 KTILVTAFDPFGGEAINPSWEAIKPLQGSQVFGANIEICQIPCIFDTSLEHLYAAVDKYQPELVISVGQAGGRTNITVERVAININDARIPDNAGNQPIDTPVIVDGPAAYFSRLPIKTmVNALNTAGIPASVSQTAGTFVCNHVmYGLLHYLAQNTPSVRGGFIHVPYLPEQAVKDGNQSSmTLmLmTLALKIAIETAWKNTSD 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181  |  | 191       201     
                                                                                                                                                 121-MSE                   147-MSE                              184-MSE|                 
                                                                                                                                                                                                                   187-MSE               
                                                                                                                                                                                                                     189-MSE
   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 4GXH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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