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(-) Description

Title :  STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-1248
 
Authors :  W. Zhu, E. Oldfield
Date :  13 Sep 12  (Deposition) - 19 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prenyl Transferase Inhibitor Complex, Alpha-Helix, Prenyl Transferase, Cell Wall Biosynthesis, Farnesyl Diphosphate Binding, Isopentenyl Diphosphate Binding, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhu, Y. Zhang, W. Sinko, M. E. Hensler, J. Olson, K. J. Molohon, S. Lindert, R. Cao, K. Li, K. Wang, Y. Wang, Y. L. Liu, A. Sankovsky, C. A. De Oliveira, D. A. Mitchell, V. Nizet, J. A. Mccammon, E. Oldfiel
Antibacterial Drug Leads Targeting Isoprenoid Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 110 123 2013
PubMed-ID: 23248302  |  Reference-DOI: 10.1073/PNAS.1219899110

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
    Chains: B, A
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, ISPU, RTH, YAES, B0174, JW0169
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: UPP SYNTHASE, DI-TRANS,POLY-CIS-DECAPRENYLCISTRANSFERASE, DITRANS,POLYCIS-UNDECAPRENYL-DIPHOSPHATE SYNTHASE, UNDECAPRENYL DIPHOSPHATE SYNTHASE, UDS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
10YW3Ligand/Ion2-{[3-(DECYLOXY)BENZOYL]AMINO}-5-NITROBENZOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:51 , VAL B:54 , SER B:55 , LEU B:93 , GLU B:96 , LEU B:100 , HIS B:103 , 0YW B:302BINDING SITE FOR RESIDUE 0YW B 301
2AC2SOFTWAREALA B:47 , ARG B:51 , PHE B:89 , ALA B:142 , ASN B:144 , 0YW B:301BINDING SITE FOR RESIDUE 0YW B 302
3AC3SOFTWAREALA A:47 , VAL A:50 , ARG A:51 , VAL A:54 , SER A:55 , ASN A:59 , PHE A:89 , GLU A:96 , SER A:99 , LEU A:100 , HIS A:103 , VAL A:105BINDING SITE FOR RESIDUE 0YW A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H2O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2O)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2O)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains d4h2oa_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh..hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2o A  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR 239
                                    26        36        46        56        66    ||  88        98       108       118       128       138       148       158  ||   173       183       193       203       213       223       233      
                                                                                 71|                                                                          161|                                                                        
                                                                                  84                                                                           167                                                                        


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains d4h2ob_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh............eeee..................eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2o B  14 PAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR 239
                                    23        33        43        53        63        89        99       109       119       129       139       149       159     ||171       181       191       201       211       221       231        
                                                                                     72|                                                                         165|                                                                       
                                                                                      89                                                                          168
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2O)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4h2o
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  2.5.1.31
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 Related Entries

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

UniProtKB/Swiss-Prot
        UPPS_ECOLI | P60472: 1jp3 1ueh 1v7u 1x06 1x07 1x08 1x09 2e98 2e99 2e9a 2e9c 2e9d 3qas 3sgv 3sgx 3sh0 3th8 3wyj 4h2j 4h2m 4h38 4h3a 4h3c 5cqb 5cqj

(-) Related Entries Specified in the PDB File

4h2j 4h2m 4h38 4h3a 4h3c