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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD BOUND MDH2
 
Authors :  Y. M. Eo, B. G. Han, H. C. Ahn
Date :  08 Oct 14  (Deposition) - 25 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Mdh2, Tca Cycle, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. M. Eo, B. G. Han, H. C. Ahn
Crystal Structure Of Nad Bound Mdh2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE, MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MDH2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:33 , GLY A:34 , GLY A:35 , ILE A:36 , TYR A:56 , ASP A:57 , ILE A:58 , PRO A:99 , ALA A:100 , GLY A:101 , VAL A:102 , PRO A:103 , LEU A:113 , ASN A:117 , ILE A:120 , ILE A:140 , ALA A:141 , ASN A:142 , VAL A:169 , HIS A:200 , ALA A:247 , MET A:251 , PO4 A:402 , PO4 A:403 , HOH A:510 , HOH A:515 , HOH A:520binding site for residue NAD A 401
02AC2SOFTWAREPRO A:103 , ARG A:104 , ARG A:110 , ASN A:142 , SER A:246 , NAD A:401 , PO4 A:403binding site for residue PO4 A 402
03AC3SOFTWAREARG A:104 , ARG A:110 , ASN A:142 , ARG A:176 , HIS A:200 , GLY A:234 , NAD A:401 , PO4 A:402binding site for residue PO4 A 403
04AC4SOFTWARESER B:33 , GLY B:34 , GLY B:35 , ILE B:36 , TYR B:56 , ASP B:57 , ILE B:58 , PRO B:99 , ALA B:100 , GLY B:101 , VAL B:102 , PRO B:103 , ASN B:117 , ILE B:120 , ILE B:140 , ASN B:142 , VAL B:169 , HIS B:200 , ALA B:247 , THR B:248 , MET B:251 , PO4 B:402 , PO4 B:403 , HOH B:511binding site for residue NAD B 401
05AC5SOFTWAREPRO B:103 , ARG B:104 , LEU B:113 , ASN B:142 , SER B:246 , NAD B:401 , PO4 B:403binding site for residue PO4 B 402
06AC6SOFTWAREARG B:104 , ARG B:110 , ASN B:142 , ARG B:176 , HIS B:200 , GLY B:234 , NAD B:401 , PO4 B:402binding site for residue PO4 B 403
07AC7SOFTWARESER C:33 , GLY C:34 , GLY C:35 , ILE C:36 , TYR C:56 , ASP C:57 , ILE C:58 , PRO C:99 , ALA C:100 , GLY C:101 , VAL C:102 , PRO C:103 , ASN C:117 , ILE C:140 , ASN C:142 , VAL C:169 , HIS C:200 , ALA C:247 , THR C:248 , MET C:251 , PO4 C:402 , PO4 C:403 , HOH C:505 , HOH C:507 , HOH C:508binding site for residue NAD C 401
08AC8SOFTWAREPRO C:103 , ARG C:104 , LEU C:113 , ASN C:142 , SER C:246 , NAD C:401 , PO4 C:403binding site for residue PO4 C 402
09AC9SOFTWAREARG C:104 , ARG C:110 , ASN C:142 , ARG C:176 , HIS C:200 , GLY C:234 , NAD C:401 , PO4 C:402binding site for residue PO4 C 403
10AD1SOFTWARESER D:33 , GLY D:34 , GLY D:35 , ILE D:36 , TYR D:56 , ASP D:57 , ILE D:58 , PRO D:99 , ALA D:100 , GLY D:101 , VAL D:102 , PRO D:103 , ASN D:117 , ILE D:120 , ILE D:140 , ASN D:142 , VAL D:169 , HIS D:200 , ALA D:247 , THR D:248 , MET D:251 , PO4 D:402 , PO4 D:403 , HOH D:504binding site for residue NAD D 401
11AD2SOFTWAREARG D:104 , ARG D:110 , ASN D:142 , ARG D:176 , HIS D:200 , GLY D:234 , NAD D:401 , PO4 D:403binding site for residue PO4 D 402
12AD3SOFTWAREPRO D:103 , ARG D:104 , ASN D:142 , SER D:246 , NAD D:401 , PO4 D:402binding site for residue PO4 D 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asn A:142 -Pro A:143
2Thr A:213 -Pro A:214
3Asn B:142 -Pro B:143
4Thr B:213 -Pro B:214
5Asn C:142 -Pro C:143
6Thr C:213 -Pro C:214
7Asn D:142 -Pro D:143
8Thr D:213 -Pro D:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WLV)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhh......eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlv A  24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
                                    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       323       333    


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeeeee..hhhhhhhhhh......eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlv B  24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
                                    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       323       333    


Chain C from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh.....eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhh..hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlv C  24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
                                    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       323       333    


Chain D from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh.....eeeeee...hhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlv D  24 NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTL 337
                                    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       323       333
   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 4WLV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        MDHM_HUMAN | P40926: 2dfd 4wle 4wlf 4wln 4wlo 4wlu

(-) Related Entries Specified in the PDB File

4wle 4wlf 4wln 4wlo 4wlu