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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DIPEPTIDYL-PEPTIDASE VI (BT_1314) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.10 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  07 Dec 10  (Deposition) - 02 Feb 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Proteinase Fold, Sh3-Like Barrel, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Dipeptidyl-Peptidase Vi (Bt_1314) From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 1 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDYL-PEPTIDASE VI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: BT_1314
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4OCS4Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:42 , ARG A:44 , HOH A:423 , TRP B:193BINDING SITE FOR RESIDUE CL A 330
2AC2SOFTWARESER A:54 , TYR A:80 , ASP A:202 , SER A:204 , ARG A:220 , ASP A:221 , HOH A:400BINDING SITE FOR RESIDUE GOL A 331
3AC3SOFTWAREASP A:79 , LEU A:323 , HOH A:388 , HOH A:445BINDING SITE FOR RESIDUE GOL A 334
4AC4SOFTWARELYS A:64 , GLN A:75 , ASP A:79 , TYR A:324BINDING SITE FOR RESIDUE GOL A 335
5AC5SOFTWARETRP A:193 , ASN B:42 , ARG B:44 , HOH B:532BINDING SITE FOR RESIDUE CL B 329
6AC6SOFTWARESER B:54 , ALA B:194 , ASP B:202 , SER B:204 , ARG B:220 , ASP B:221 , HOH B:424 , HOH B:772BINDING SITE FOR RESIDUE GOL B 332
7AC7SOFTWAREASP B:79 , ASN B:322 , LEU B:323 , HOH B:414 , HOH B:538BINDING SITE FOR RESIDUE GOL B 333

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PVQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PVQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PVQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PVQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3PVQ)

(-) 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:297
 aligned with Q8A860_BACTN | Q8A860 from UniProtKB/TrEMBL  Length:328

    Alignment length:297
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       
         Q8A860_BACTN    32 AYGVVHISVCNMRDEGKFTSGMSTQALLGMPVKVLQYTGWYEIQTPDDYTGWVHRMVITPMSKEKYDEWNRAEKIVVTSHYGFTYEKPDDDSQTVSDVVAGNRLKWEGSKGHFYKVSYPDGRQAYISRHISQPESKWRASLKQDAESIIKTAYTMIGIPYLWAGTSSKGVDCSGLVRTVLFMHDIIIPRDASQQAYVGERIEIAPDFSNVQRGDLVFFGRKATADRKEGISHVGIYLGNKRFIHALGDVHISSFDPEDECYDEFNTGRLLFATRFLPYINKEKGMNTTDHNLYYLHH 328
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeee........eeeeee...eeeeeee..eeeee.....eeeee...eeeehhhhhhhhhhh.eeee...eeeee........eeeeee...eeeeeeee..eeeee.....eeeee...eeehhhhhhhh..hhhhhhhhhhh..........ee..eehhhhhhhhhhhh..ee...hhhhhh...eee.............eeeeee........eeeeeeeeee..eeeee...eeeee........hhhhhh.eeeeeehhhhh......ee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pvq A  32 AYGVVHISVCNmRDEGKFTSGmSTQALLGmPVKVLQYTGWYEIQTPDDYTGWVHRmVITPmSKEKYDEWNRAEKIVVTSHYGFTYEKPDDDSQTVSDVVAGNRLKWEGSKGHFYKVSYPDGRQAYISRHISQPESKWRASLKQDAESIIKTAYTmIGIPYLWAGTSSKGVDcSGLVRTVLFmHDIIIPRDASQQAYVGERIEIAPDFSNVQRGDLVFFGRKATADRKEGISHVGIYLGNKRFIHALGDVHISSFDPEDEcYDEFNTGRLLFATRFLPYINKEKGmNTTDHNLYYLHH 328
                                    41 |      51 |      61        71        81     |  91|      101       111       121       131       141       151       161       171       181    |  191       201 |     211 |     221       231       241       251       261       271       281       291       301       311    |  321       
                                      43-MSE    53-MSE  61-MSE                    87-MSE|                                                                                           186-MSE          203-OCS   213-MSE                                                                       291-OCS                  316-MSE        
                                                                                       92-MSE                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q8A860_BACTN | Q8A860 from UniProtKB/TrEMBL  Length:328

    Alignment length:297
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       
         Q8A860_BACTN    32 AYGVVHISVCNMRDEGKFTSGMSTQALLGMPVKVLQYTGWYEIQTPDDYTGWVHRMVITPMSKEKYDEWNRAEKIVVTSHYGFTYEKPDDDSQTVSDVVAGNRLKWEGSKGHFYKVSYPDGRQAYISRHISQPESKWRASLKQDAESIIKTAYTMIGIPYLWAGTSSKGVDCSGLVRTVLFMHDIIIPRDASQQAYVGERIEIAPDFSNVQRGDLVFFGRKATADRKEGISHVGIYLGNKRFIHALGDVHISSFDPEDECYDEFNTGRLLFATRFLPYINKEKGMNTTDHNLYYLHH 328
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------NLPC_P60-3pvqB01 B:188-302                                                                                         -------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------NLPC_P60-3pvqB02 B:188-302                                                                                         -------------------------- Pfam domains (2)
         Sec.struct. author .eeee...eeeee........eeeeee...eeeeeee..eeeee.....eeeee...eeeehhhhhhhhhhh.eeee...eeeee........eeeeee...eeeeeeee..eeeee.....eeeee...eeehhhhhhhh..hhhhhhhhhhh..........ee..eehhhhhhhhhhhh..ee...hhhhhh...eee.............eeeeee........eeeeeeeeee..eeeee...eeeee........hhhhhh.eeeeeehhhhh......ee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pvq B  32 AYGVVHISVCNmRDEGKFTSGmSTQALLGmPVKVLQYTGWYEIQTPDDYTGWVHRmVITPmSKEKYDEWNRAEKIVVTSHYGFTYEKPDDDSQTVSDVVAGNRLKWEGSKGHFYKVSYPDGRQAYISRHISQPESKWRASLKQDAESIIKTAYTmIGIPYLWAGTSSKGVDcSGLVRTVLFmHDIIIPRDASQQAYVGERIEIAPDFSNVQRGDLVFFGRKATADRKEGISHVGIYLGNKRFIHALGDVHISSFDPEDEcYDEFNTGRLLFATRFLPYINKEKGmNTTDHNLYYLHH 328
                                    41 |      51 |      61        71        81     |  91|      101       111       121       131       141       151       161       171       181    |  191       201 |     211 |     221       231       241       251       261       271       281       291       301       311    |  321       
                                      43-MSE    53-MSE  61-MSE                    87-MSE|                                                                                           186-MSE          203-OCS   213-MSE                                                                       291-OCS                  316-MSE        
                                                                                       92-MSE
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  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  (0, 0)

(no "SCOP Domain" information available for 3PVQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PVQ)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3PVQ)

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