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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTATE/MALATE DEHYDROGENASE FROM BRUCELLA MELITENSIS IN COMPLEX WITH ADP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  31 Mar 09  (Deposition) - 14 Apr 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F  (2x)
Keywords :  Lactate/Malate Dehydrogenase, Brucella Melitensis, Nad, Oxidoreductase, Tricarboxylic Acid Cycle, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, B. Staker
Crystal Structure Of Lactate/Malate Dehydrogenase From Brucella Melitensis In Complex With Adp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D, E, F
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MDH, BAB1_1927
    Organism Scientific: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308
    Organism Taxid: 359391

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCD  
Biological Unit 2 (2x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , MET A:13 , ILE A:14 , ASP A:34 , ILE A:35 , ALA A:79 , GLY A:80 , GLN A:102 , HOH A:340 , HOH A:354 , HOH A:359 , HOH A:391 , HOH A:448 , HOH A:528 , HOH A:831 , HOH A:1210BINDING SITE FOR RESIDUE ADP A 401
2AC2SOFTWAREGLY B:12 , MET B:13 , ILE B:14 , PHE B:33 , ASP B:34 , ILE B:35 , ALA B:79 , GLY B:80 , GLN B:102 , HOH B:338 , HOH B:372 , HOH B:378 , HOH B:385 , HOH B:390 , HOH B:990 , HOH B:1076 , HOH B:1236BINDING SITE FOR RESIDUE ADP B 401
3AC3SOFTWAREGLY C:12 , MET C:13 , ILE C:14 , PHE C:33 , ASP C:34 , ILE C:35 , ALA C:79 , GLY C:80 , GLN C:102 , HOH C:323 , HOH C:350 , HOH C:360 , HOH C:366 , HOH C:727 , HOH C:1258BINDING SITE FOR RESIDUE ADP C 401
4AC4SOFTWAREGLY D:12 , MET D:13 , ILE D:14 , ASP D:34 , ILE D:35 , ALA D:79 , GLY D:80 , VAL D:99 , GLN D:102 , HOH D:332 , HOH D:336 , HOH D:338 , HOH D:586 , HOH D:635 , HOH D:841 , HOH D:1102BINDING SITE FOR RESIDUE ADP D 401
5AC5SOFTWAREGLY E:12 , MET E:13 , ILE E:14 , PHE E:33 , ASP E:34 , ILE E:35 , ALA E:79 , GLY E:80 , VAL E:99 , GLN E:102 , HOH E:341 , HOH E:445 , HOH E:523 , HOH E:600 , HOH E:670 , HOH E:1108 , HOH E:1298 , HOH E:1299BINDING SITE FOR RESIDUE ADP E 401
6AC6SOFTWAREGLY F:12 , MET F:13 , ILE F:14 , ASP F:34 , ILE F:35 , ALA F:79 , GLY F:80 , VAL F:99 , GLN F:102 , HOH F:324 , HOH F:345 , HOH F:363 , HOH F:414 , HOH F:645 , HOH F:730 , HOH F:959 , HOH F:1031BINDING SITE FOR RESIDUE ADP F 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asn A:121 -Pro A:122
2Asn B:121 -Pro B:122
3Asn C:121 -Pro C:122
4Asn D:121 -Pro D:122
5Asn E:121 -Pro E:122
6Asn F:121 -Pro F:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GVI)

(-) 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:314
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
               SCOP domains d3gvia1 A:2-144 automated matches                                                                                                              d3gvia2 A:145-320 automated matches                                                                                                                                              SCOP domains
               CATH domains 3gviA01 A:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviA02 A:146-320 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvi A   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                                                                             84    90                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
               SCOP domains d3gvib1 B:2-144 automated matches                                                                                                              d3gvib2 B:145-320 automated matches                                                                                                                                              SCOP domains
               CATH domains 3gviB01 B:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviB02 B:146-320 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eeeehhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvi B   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                                                                             84    90                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:314
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
               SCOP domains d3gvic1 C:2-144 automated matches                                                                                                              d3gvic2 C:145-320 automated matches                                                                                                                                              SCOP domains
               CATH domains 3gviC01 C:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviC02 C:146-320 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----.hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eeeehhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvi C   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                                                                             84    90                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:313
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSL 319
               SCOP domains d3gvid1 D:2-144 automated matches                                                                                                              d3gvid2 D:145-319 automated matches                                                                                                                                             SCOP domains
               CATH domains 3gviD01 D:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviD02 D:146-319 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gvi D   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSL 319
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
                                                                                                             84    90                                                                                                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:314
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
               SCOP domains d3gvie1 E:2-144 automated matches                                                                                                              d3gvie2 E:145-320 automated matches                                                                                                                                              SCOP domains
               CATH domains 3gviE01 E:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviE02 E:146-320 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvi E   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                                                                             84    90                                                                                                                                                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:314
 aligned with MDH_BRUA2 | Q2YLR9 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
            MDH_BRUA2     2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKPGMSRDDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
               SCOP domains d3gvif1 F:2-144 automated matches                                                                                                              d3gvif2 F:145-320 automated matches                                                                                                                                              SCOP domains
               CATH domains 3gviF01 F:2-145 NAD(P)-binding Rossmann-like Domain                                                                                             3gviF02 F:146-320 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......-----hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvi F   2 ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESSPVDGFDAKFTGANDYAAIEGADVVIVTAGVPRK-----DDLLGINLKVMEQVGAGIKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYFLSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQDKLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPVAAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVAGLCEACIGIAPSLK 320
                                    11        21        31        41        51        61        71        81  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                                                                                                             84    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  (2, 12)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 12)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (MDH_BRUA2 | Q2YLR9)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    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.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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 Related Entries

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        MDH_BRUA2 | Q2YLR9: 3gvh

(-) Related Entries Specified in the PDB File

3gvh NATIVE STRUCTURE WITH NAD BOUND RELATED ID: BRABA.00005.A RELATED DB: TARGETDB