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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS MALATE DEHYDROGENASE IN COMPLEX WITH NAD
 
Authors :  C. -H. Hsu, C. -H. Hong, Y. -Y. Chang
Date :  25 Apr 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Hung, T. S. Hwang, Y. Y. Chang, H. R. Luo, S. P. Wu, C. H. Hsu
Crystal Structures And Molecular Dynamics Simulations Of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion For Co-Substrate Binding.
Plos One V. 8 83091 2013
PubMed-ID: 24386145  |  Reference-DOI: 10.1371/JOURNAL.PONE.0083091

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET-21
    Fragment: MALATE DEHYDROGENASE
    Gene: MDH
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:162 , HIS A:187 , GLY A:226 , SER A:237 , HOH A:525BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWARELYS A:305 , ARG A:306 , ARG C:203 , GLU C:207BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREGLY A:31 , LYS A:32 , ARG A:250BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREARG B:162 , HIS B:187 , GLY B:226 , SER B:237BINDING SITE FOR RESIDUE SO4 B 401
05AC5SOFTWAREPHE B:302 , LYS B:305 , ARG B:306 , ARG D:203 , GLU D:207BINDING SITE FOR RESIDUE SO4 B 402
06AC6SOFTWAREGLY B:31 , LYS B:32 , ARG B:250BINDING SITE FOR RESIDUE SO4 B 403
07AC7SOFTWAREARG C:162 , HIS C:187 , GLY C:226 , SER C:237 , HOH C:532BINDING SITE FOR RESIDUE SO4 C 401
08AC8SOFTWAREGLY C:31 , LYS C:32 , ARG C:250 , HOH C:557BINDING SITE FOR RESIDUE SO4 C 402
09AC9SOFTWAREARG D:162 , HIS D:187 , GLY D:226 , SER D:237 , HOH D:515BINDING SITE FOR RESIDUE SO4 D 401
10BC1SOFTWAREGLY D:31 , LYS D:32 , ARG D:250BINDING SITE FOR RESIDUE SO4 D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:131 -Pro A:132
2Asn B:131 -Pro B:132
3Asn C:131 -Pro C:132
4Asn D:131 -Pro D:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KDF)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4kdfa1 A:1-154 Malate dehydrogenase                                                                                                             d4kdfa2 A:155-326 Malate dehydrogenase                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee......hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdf A   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGL 326
                                    10        20        30        40        50        60        70        80        90||     109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       
                                                                                                                     91|                                                                                                                                                                                                                                 
                                                                                                                     101                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4kdfb1 B:1-154 Malate dehydrogenase                                                                                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee......hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeee...........eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kdf B   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGL 326
                                    10        20        30        40        50        60        70        80        90||     109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       
                                                                                                                     91|                                                                                                                                                                                                                                 
                                                                                                                     101                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4kdfc1 C:1-154 Malate dehydrogenase                                                                                                              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee.......hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kdf C   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGL 326
                                    10        20        30        40        50        60        70        80        90 ||    108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318        
                                                                                                                      92|                                                                                                                                                                                                                                 
                                                                                                                      101                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4kdfd1 D:1-154 Malate dehydrogenase                                                                                                              d4kdfd2 D:155-326 Malate dehydrogenase                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhh....eeee.......hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kdf D   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGL 326
                                    10        20        30        40        50        60        70        80        90 ||    108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318        
                                                                                                                      92|                                                                                                                                                                                                                                 
                                                                                                                      101
   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, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        MDH_THETH | P10584: 1bdm 1bmd 1iz9 1wze 1wzi 1y7t 2cvq 4kde

(-) Related Entries Specified in the PDB File

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