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(-) Description

Title :  CRYSTAL STRUCTURE OF AN L,D-CARBOXYPEPTIDASE DACB FROM STREPTOCOCCUS PNEUMONIA
 
Authors :  Y. H. Yang, J. Zhang, Y. L. Jiang, C. Z. Zhou, Y. Chen
Date :  02 Dec 13  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Hydrolase, Zinc-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Yang, J. Zhang, Y. L. Jiang, C. Z. Zhou, Y. Chen
Crystal Structure Of An L, D-Carboxypeptidase Dacb From Streptococcus Pneumonia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: B, A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-238
    Gene: SP_0629
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: L,D-CARBOXYPEPTIDASE DACB

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x): A  
Biological Unit 4 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3ZN3Ligand/IonZINC ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:153 , ASP B:160 , GLU B:204 , HIS B:207 , HOH B:406 , HOH B:416BINDING SITE FOR RESIDUE ZN B 301
02AC2SOFTWAREARG B:120 , GLN B:125 , ALA B:146 , SER B:151 , HIS B:153 , GLU B:204 , GOL B:303 , HOH B:416BINDING SITE FOR RESIDUE ACT B 302
03AC3SOFTWARETYR B:132 , TYR B:144 , SER B:145 , GLU B:204 , ACT B:302 , HOH B:406 , HOH B:465BINDING SITE FOR RESIDUE GOL B 303
04AC4SOFTWAREHIS A:153 , ASP A:160 , GLU A:204 , HIS A:207 , HOH A:413 , HOH A:434BINDING SITE FOR RESIDUE ZN A 301
05AC5SOFTWAREARG A:120 , GLN A:125 , ALA A:146 , SER A:151 , HIS A:153 , HOH A:417 , HOH A:434 , HOH A:505BINDING SITE FOR RESIDUE ACT A 302
06AC6SOFTWAREHIS A:115 , TYR A:116 , HOH A:527 , PRO B:88 , GLY B:89 , GLU B:90 , ASN B:91 , HOH B:494BINDING SITE FOR RESIDUE GOL A 303
07AC7SOFTWARELYS A:78 , HIS A:79 , TYR A:236 , VAL A:237 , HOH A:492 , TYR B:185 , HOH B:523BINDING SITE FOR RESIDUE GOL A 304
08AC8SOFTWAREHIS C:153 , ASP C:160 , GLU C:204 , HIS C:207 , HOH C:413 , HOH C:430BINDING SITE FOR RESIDUE ZN C 301
09AC9SOFTWAREARG C:120 , GLN C:125 , SER C:145 , ALA C:146 , SER C:151 , HIS C:153 , GLU C:204 , HOH C:430 , HOH C:459BINDING SITE FOR RESIDUE ACT C 302
10BC1SOFTWAREGLU C:107 , TYR C:185 , HOH C:434 , HOH C:449 , HOH C:524BINDING SITE FOR RESIDUE GOL C 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NT9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NT9)

(-) Exons   (0, 0)

(no "Exon" information available for 4NT9)

(-) Sequences/Alignments

Asymmetric 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:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee.......hhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt9 A  54 KAEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNQDGKAAADRYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAASGLSLEEYYGFEGGDYV 237
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee.......hhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt9 B  54 KAEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNQDGKAAADRYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAASGLSLEEYYGFEGGDYV 237
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    


Chain C from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeee....eeee...............hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee.......hhhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt9 C  54 KAEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNQDGKAAADRYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAASGLSLEEYYGFEGGDYV 237
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   Legend:   → Mismatch (orange background)
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  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 4NT9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NT9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NT9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NT9)

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