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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATITVE SHORT CHAIN DEHYDROGENASE FROM SHIGELLA FLEXNERI 2A STR. 301 COMPLEXED WITH NADP
 
Authors :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. A York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Apr 09  (Deposition) - 14 Apr 09  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, Nysgxrc, Short Chain Dehydrogenase, Nadp, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putatitve Short Chain Dehydrogenase From Shigella Flexneri 2A Str. 301 Complexed With Nadp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YCIK, S1358, SF1273
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: 301

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , SER A:19 , ASP A:20 , GLY A:21 , ILE A:22 , ARG A:42 , ASN A:43 , LEU A:67 , ASP A:68 , LEU A:69 , ASN A:97 , ALA A:98 , GLY A:99 , ILE A:121 , THR A:148 , SER A:149 , TYR A:163 , LYS A:167 , PRO A:192 , GLY A:193 , GLY A:194 , THR A:195 , THR A:197 , MET A:199 , ARG A:200 , HOH A:256 , HOH A:332 , HOH A:335 , HOH A:345 , HOH A:352 , HOH A:376 , HOH A:405 , HOH A:415 , HOH A:436BINDING SITE FOR RESIDUE NAP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GY0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GY0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GY0)

(-) Exons   (0, 0)

(no "Exon" information available for 3GY0)

(-) 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:239
 aligned with Q83RM3_SHIFL | Q83RM3 from UniProtKB/TrEMBL  Length:252

    Alignment length:239
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235         
         Q83RM3_SHIFL     6 KQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQINVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQP 244
               SCOP domains d3gy0a_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains 3gy0A00 A:4-242 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gy0 A   4 KQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQINVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQP 242
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GY0)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q83RM3_SHIFL | Q83RM3)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        Q83RM3_SHIFL | Q83RM3: 3e9q 3f5s

(-) Related Entries Specified in the PDB File

3f5s APO-ENZYME RELATED ID: NYSGXRC-13837C RELATED DB: TARGETDB