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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION
 
Authors :  J. J. Birktoft, L. J. Banaszak
Date :  12 Apr 89  (Deposition) - 19 Apr 89  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase(Nad(A)-Choh(D)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Birktoft, G. Rhodes, L. J. Banaszak
Refined Crystal Structure Of Cytoplasmic Malate Dehydrogenase At 2. 5-A Resolution.
Biochemistry V. 28 6065 1989
PubMed-ID: 2775751  |  Reference-DOI: 10.1021/BI00440A051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOPLASMIC MALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.37
    Engineered: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:130 , LEU A:157 , ARG A:161 , HIS A:186 , GLY A:230 , SER A:241 , NAD A:335 , HOH A:445 , HOH A:540BINDING SITE FOR RESIDUE SO4 A 334
2AC2SOFTWAREASN B:130 , HIS B:186 , NAD B:335 , HOH B:469BINDING SITE FOR RESIDUE SO4 B 334
3AC3SOFTWAREGLY A:10 , ALA A:12 , GLY A:13 , GLN A:14 , ILE A:15 , ASP A:41 , ILE A:42 , VAL A:86 , GLY A:87 , SER A:88 , MET A:89 , PRO A:90 , VAL A:128 , GLY A:129 , ASN A:130 , LEU A:154 , HIS A:186 , SER A:241 , ALA A:245 , SO4 A:334 , HOH A:362 , HOH A:366 , HOH A:370 , HOH A:396 , HOH A:424 , HOH A:541 , HOH A:552 , GLY B:301BINDING SITE FOR RESIDUE NAD A 335
4AC4SOFTWAREGLY B:10 , ALA B:12 , GLY B:13 , GLN B:14 , ILE B:15 , ASP B:41 , ILE B:42 , MET B:45 , VAL B:86 , SER B:88 , VAL B:128 , GLY B:129 , ASN B:130 , LEU B:154 , LEU B:157 , HIS B:186 , SER B:240 , SO4 B:334 , HOH B:358 , HOH B:475 , HOH B:476 , HOH B:511 , HOH B:543 , HOH B:544 , HOH B:560BINDING SITE FOR RESIDUE NAD B 335

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:130 -Pro A:131
2Asn B:130 -Pro B:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MDH)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -d4mdha1 A:1-154 Malate dehydrogenase                                                                                                                      d4mdha2 A:155-333 Malate dehydrogenase                                                                                                                                              SCOP domains
               CATH domains -4mdhA01 A:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      4mdhA02 A:154-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhh..eeeee................hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeeee..........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdh A   0 xSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA 333
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                            |                                                                                                                                                                                                                                                                                                                                             
                            0-ACE                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -d4mdhb1 B:1-154 Malate dehydrogenase                                                                                                                      d4mdhb2 B:155-333 Malate dehydrogenase                                                                                                                                              SCOP domains
               CATH domains -4mdhB01 B:1-153 NAD(P)-binding Rossmann-like Domain                                                                                                      4mdhB02 B:154-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhh..eeeee................hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeeeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeeee..........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdh B   0 xSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA 333
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                            0-ACE
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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