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(-) Description

Title :  E. COLI MALATE DEHYDROGENASE WITH THE INHIBITOR 6DHNAD
 
Authors :  K. M. Meneely, A. L. Lamb, G. R. Moran
Date :  21 Jun 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Malate, Dehydrogenase, 6Dhnad, Inhibitor, Beta- 6-Dihydronicotimide Adenine Dinucleotide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Beaupre, J. V. Roman, M. R. Hoag, K. M. Meneely, N. R. Silvaggi, A. L. Lamb, G. R. Moran
Ligand Binding Phenomena That Pertain To The Metabolic Function Of Renalase.
Arch. Biochem. Biophys. V. 612 46 2016
PubMed-ID: 27769837  |  Reference-DOI: 10.1016/J.ABB.2016.10.011

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MDH, B3236, JW3205
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
16V02Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(5-AMINOCARBONYL-2~{H}-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYLHYDROGEN PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:9 , GLY A:10 , GLY A:11 , ILE A:12 , TYR A:33 , ASP A:34 , ILE A:35 , SER A:76 , ALA A:77 , GLY A:78 , ASN A:94 , ILE A:97 , ASN A:100 , LEU A:101 , ILE A:117 , ASN A:119 , VAL A:121 , VAL A:146 , HIS A:177 , ALA A:223 , THR A:224 , MET A:227 , HOH A:509 , HOH A:538 , HOH A:548 , HOH A:560 , HOH A:589 , HOH A:612 , HOH A:625 , HOH A:675binding site for residue 6V0 A 401
2AC2SOFTWAREGLY B:7 , GLY B:10 , GLY B:11 , ILE B:12 , TYR B:33 , ASP B:34 , ILE B:35 , SER B:76 , ALA B:77 , GLY B:78 , ILE B:97 , ASN B:100 , LEU B:101 , ILE B:117 , ASN B:119 , VAL B:121 , VAL B:146 , HIS B:177 , ALA B:223 , THR B:224 , MET B:227 , HOH B:518 , HOH B:532 , HOH B:538 , HOH B:553 , HOH B:569 , HOH B:575 , HOH B:594 , HOH B:605 , HOH B:653binding site for residue 6V0 B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:119 -Pro A:120
2Asn B:119 -Pro B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KKA)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh....eeeeee....hhhhhh...eeee....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kka A   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVN 311
                                    10        20        30        40        50        60        70       |91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
                                                                                                        78|                                                                                                                                                                                                                             
                                                                                                         90                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh....eeeeee....hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kka B   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVN 311
                                    10        20        30        40        50        60        70        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
                                                                                                         79|                                                                                                                                                                                                                             
                                                                                                          90
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDH_ECOLI | P61889: 1cme 1emd 1ib6 1ie3 2cmd 2pwz 3hhp

(-) Related Entries Specified in the PDB File

5kkc