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(-) Description

Title :  CRYSTAL STRUCTURE OF NADP-DEPENDENT DEHYDROGENASE FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH NADPH AND OXALATE
 
Authors :  P. Sroka, O. A. Gasiorowska, K. B. Handing, I. G. Shabalin, P. J. Porebsk B. S. Hillerich, J. Bonanno, S. C. Almo, W. Minor, New York Structura Genomics Research Consortium (Nysgrc)
Date :  26 Mar 15  (Deposition) - 08 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  New York Structural Genomics Research Consortium, Nadph, Oxalate, Psi-Biology, Nysgrc, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sroka, O. A. Gasiorowska, K. B. Handing, I. G. Shabalin, W. Minor
Crystal Structure Of Nadp-Dependent Dehydrogenase From Sinorhizobium Meliloti
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAD-DEPENDENT DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: R00152, SMC02828
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: RHIZOBIUM MELILOTI (STRAIN 1021)
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL2Ligand/IonGLYCEROL
4NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5OXD2Ligand/IonOXALIC ACID
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL4Ligand/IonGLYCEROL
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5OXD4Ligand/IonOXALIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:275 , ASN A:276 , HOH A:550binding site for residue CL A 401
2AC2SOFTWARETRP A:53 , GLY A:73 , ALA A:74 , GLY A:75 , ARG A:234 , HIS A:282 , NDP A:407 , HOH A:641 , HOH A:700binding site for residue OXD A 402
3AC3SOFTWAREHIS A:117 , ARG A:118 , GLU A:121 , TYR A:278 , HOH A:659binding site for residue OXD A 403
4AC4SOFTWAREGLY A:46 , ASP A:65 , ARG A:220 , SER A:249 , GLY A:250binding site for residue EPE A 404
5AC5SOFTWAREPRO A:57 , ASP A:58 , PRO A:83 , ALA A:241 , HOH A:515 , HOH A:526 , HOH A:724binding site for residue GOL A 405
6AC6SOFTWAREHIS A:113 , GLN A:116 , VAL A:228 , HOH A:509 , HOH A:579 , HOH A:775binding site for residue GOL A 406
7AC7SOFTWAREARG A:92 , MET A:102 , MET A:147 , GLY A:148 , VAL A:149 , LEU A:150 , TRP A:168 , SER A:169 , ARG A:170 , SER A:171 , ARG A:173 , LEU A:199 , LEU A:200 , PRO A:201 , ALA A:232 , GLY A:233 , ARG A:234 , ASP A:258 , HIS A:282 , ALA A:284 , ALA A:285 , TYR A:319 , OXD A:402 , HOH A:536 , HOH A:546 , HOH A:558 , HOH A:565 , HOH A:574 , HOH A:599 , HOH A:625 , HOH A:629 , HOH A:651 , HOH A:684 , HOH A:685 , HOH A:743 , HOH A:761binding site for residue NDP A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z0P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z0P)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z0P)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhh.......eee..hhhhh........eeeee....hhhhhh....eeee......hhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh.eeeee..hhhhhhhhhhhhhh..eeeee..........eeehhhhhhhhhhhh.eeee....hhhhh...hhhhhh...........eeee..hhhhhhhhhhhhhhhhh...eeee...........hhhhhh..eee........hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0p A   4 KSPVIVDLKFIPEEVEAALAGAFPGREVIDLADPAHQERDLSGIDYAVVWKSAPDLFSRAPDLKVVFSGGAGVDHVLTLPGLPDVPLVRFVDRTLTTRMSEWVMMQCLLHLRQHRAYEALAKKHEWRDLSQPEAADVTVGIMGMGVLGQDAARKLAAMGFKVIGWSRSKRVIEGVETYDAAGLDAFLGRTDFLVGLLPLTPDTRGIFNAALFAKLSRNGPFGAPVFINAGRGGSQVEADILECLDSGVLGGASLDVFEREPLSPESRFWDMPNVYVTPHVAASSDVRALFVHVEHQIARFESGLPLEHVVDKVAGY 319
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   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 4Z0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z0P)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q92T34_RHIME | Q92T34: 4weq 5unn

(-) Related Entries Specified in the PDB File

4weq COMPLEX WITH NADP AND SULFATE RELATED ID: NYSGRC-011884 RELATED DB: TARGETTRACK