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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM RHODOPSEUDOMONAS PALUSTRIS
 
Authors :  Y. Patskovsky, R. Toro, C. Morano, J. Freeman, S. Miller, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  24 Apr 09  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Dehydrogenase, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, C. Morano, S. Miller, J. Freeman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Short-Chain Dehydrogenase From Rhodopseudomonas Palustris
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHORT CHAIN DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPA0021
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1UNL3Ligand/IonUNKNOWN LIGAND

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:241 , ARG D:169 , MET D:172 , HOH D:449BINDING SITE FOR RESIDUE UNL D 251
2AC2SOFTWAREARG B:239 , TYR B:241 , ARG C:169 , MET C:172 , HOH C:450BINDING SITE FOR RESIDUE UNL C 251
3AC3SOFTWAREARG A:169 , MET A:172 , ARG D:239 , TYR D:241BINDING SITE FOR RESIDUE UNL D 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H7A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met B:212 -Pro B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H7A)

(-) Exons   (0, 0)

(no "Exon" information available for 3H7A)

(-) 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:212
 aligned with Q6NDT3_RHOPA | Q6NDT3 from UniProtKB/TrEMBL  Length:245

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q6NDT3_RHOPA     3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIIDSGVDTAWVRERREQMFGKDALANPDLLMPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
               SCOP domains d3h7aa_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.---------------------------.hhhhhhhhhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7a A   3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIID---------------------------MPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 |       -         -       212       222       232         
                                                                                                                                                                                                               184                         212                             


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q6NDT3_RHOPA | Q6NDT3 from UniProtKB/TrEMBL  Length:245

    Alignment length:240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
         Q6NDT3_RHOPA     2 TPRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIIDSGVDTAWVRERREQMFGKDALANPDLLMPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
               SCOP domains d3h7ab_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.---------------------------.hhhhhhhhhhhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h7a B   2 TPRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIID---------------------------MPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  |      -         -         -|      221       231       241
                                                                                                                                                                                                                184                         212                             


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q6NDT3_RHOPA | Q6NDT3 from UniProtKB/TrEMBL  Length:245

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q6NDT3_RHOPA     3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIIDSGVDTAWVRERREQMFGKDALANPDLLMPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
               SCOP domains d3h7ac_ C: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.---------------------------.hhhhhhhhhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7a C   3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIID---------------------------MPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 |       -         -       212       222       232         
                                                                                                                                                                                                               184                         212                             


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q6NDT3_RHOPA | Q6NDT3 from UniProtKB/TrEMBL  Length:245

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q6NDT3_RHOPA     3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIIDSGVDTAWVRERREQMFGKDALANPDLLMPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
               SCOP domains d3h7ad_ D: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.---------------------------.hhhhhhhhhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7a D   3 PRNATVAVIGAGDYIGAEIAKKFAAEGFTVFAGRRNGEKLAPLVAEIEAAGGRIVARSLDARNEDEVTAFLNAADAHAPLEVTIFNVGANVNFPILETTDRVFRKVWEMACWAGFVSGRESARLMLAHGQGKIFFTGATASLRGGSGFAAFASAKFGLRAVAQSMARELMPKNIHVAHLIID---------------------------MPPAAVAGAYWQLYQQPKSAWTFEMEIRPY 241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 |       -         -       212       222       232         
                                                                                                                                                                                                               184                         212
   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 3H7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H7A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3H7A)

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