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(-) Description

Title :  CRYSTAL STRUCTURE OF AN OXIDOREDUCTASE FROM BURKHOLDERIA VIETNAMIENSIS IN COMPLEX WITH NADP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  24 Feb 16  (Deposition) - 16 Mar 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Ssgcid, Oxidoreductase, Short Chain Dehydrogenase/Reductase Family, Nadp, Burkholderia Vietnamiensis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Mayclin, J. Abendroth, D. D. Lorimer, T. E. Edwards
Crystal Structure Of An Oxidoreductase From Burkholderia Vietnamiensis In Complex With Nadp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BUVIA.00010.K.B1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BCEP1808_2377
    Organism Scientific: BURKHOLDERIA VIETNAMIENSIS (STRAIN G4 / LMG 22486)
    Organism Taxid: 269482
    Strain: G4 / LMG 22486

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO46Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:17 , GLY A:18 , ARG A:21 , THR A:188 , ASP A:189 , ARG A:225 , HOH A:515 , HOH A:532binding site for residue SO4 A 401
02AC2SOFTWAREARG A:190 , NAP A:405 , HOH A:535 , HOH A:563 , HOH A:597 , HOH A:642binding site for residue SO4 A 402
03AC3SOFTWAREARG A:21 , ARG A:225 , HOH A:596binding site for residue EDO A 403
04AC4SOFTWAREGLN A:202 , ARG A:212 , ARG A:213binding site for residue CL A 404
05AC5SOFTWAREALA A:14 , SER A:16 , LYS A:17 , GLY A:18 , LEU A:19 , ALA A:38 , ARG A:39 , THR A:40 , CYS A:64 , ASP A:65 , ILE A:66 , THR A:67 , ASN A:88 , ALA A:89 , GLY A:90 , GLY A:91 , ILE A:138 , THR A:139 , SER A:140 , ARG A:157 , PRO A:183 , GLY A:184 , LEU A:185 , PHE A:186 , THR A:188 , ARG A:190 , SO4 A:402 , HOH A:515 , HOH A:525 , HOH A:528 , HOH A:535 , HOH A:536 , HOH A:562 , HOH A:602 , HOH A:642 , HOH A:658 , HOH A:667binding site for residue NAP A 405
06AC6SOFTWAREALA B:14 , SER B:16 , LYS B:17 , GLY B:18 , LEU B:19 , ALA B:38 , ARG B:39 , THR B:40 , CYS B:64 , ASP B:65 , ILE B:66 , THR B:67 , ASN B:88 , ALA B:89 , GLY B:90 , GLY B:91 , ILE B:138 , THR B:139 , SER B:140 , ARG B:157 , PRO B:183 , GLY B:184 , LEU B:185 , PHE B:186 , THR B:188 , ARG B:190 , ILE B:191 , HOH B:406 , HOH B:417 , HOH B:422 , HOH B:466 , HOH B:497 , HOH B:515 , HOH B:529 , HOH B:534 , HOH B:616binding site for residue NAP B 301
07AC7SOFTWAREARG A:41 , LYS B:17 , GLY B:18 , THR B:188 , ASP B:189 , ARG B:225 , HOH B:406 , HOH B:425 , HOH B:429 , HOH B:437 , HOH B:453binding site for residue SO4 B 302
08AC8SOFTWAREHIS B:-4 , ARG B:98 , ASP B:99binding site for residue EDO B 303
09AC9SOFTWAREASP A:125 , HIS B:-2 , HIS B:0binding site for residue EDO B 304
10AD1SOFTWAREARG B:212 , ARG B:213binding site for residue CL B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IDY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IDY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IDY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IDY)

(-) Exons   (0, 0)

(no "Exon" information available for 5IDY)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhh..........eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5idy A  -2 HHHMDLGIAGKTALVCAASKGLGRGCAEALAAEGVNLVIVARTRDTLERTADEIRAASNVSVATVACDITTPDGRAAALAACPQPDILVNNAGGPPPGDFRDFSHDDWIRALESNMLTPIELIRATVDGMIARGFGRIVNITSSAVKAPIDVLALSNGARSGLTGFVAGLARKVVGQGVTINNLLPGLFDTDRIATTLAAAANAQGVTVDELRARRTRDIPAGRLGTRAEFGAACAFLCSVHAGYITGQNWLLDGGAYPGTF 259
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257  


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhh..........eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5idy B  -4 HHHHHMDLGIAGKTALVCAASKGLGRGCAEALAAEGVNLVIVARTRDTLERTADEIRAASNVSVATVACDITTPDGRAAALAACPQPDILVNNAGGPPPGDFRDFSHDDWIRALESNMLTPIELIRATVDGMIARGFGRIVNITSSAVKAPIDVLALSNGARSGLTGFVAGLARKVVGQGVTINNLLPGLFDTDRIATTLAAAANAQGVTVDELRARRTRDIPAGRLGTRAEFGAACAFLCSVHAGYITGQNWLLDGGAYPGTF 259
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
   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  (0, 0)

(no "SCOP Domain" information available for 5IDY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IDY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IDY)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5IDY)

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