Malate Dehydrogenase 3D structures

3D Structures of Malate Dehydrogenase

Updated on 10-December-2025

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The holo-MDH contains NAD or its derivatives while the apo-MDH lacks it.

• Holo-MDH
  • 2dfd, 4wlv – hMDH2 +NAD – human
    
  • 7bsj, 7bsk, 7bsl – hMd2 (mutant) +NAD
    
  • 4mdh – pMDH+NAD - pig
    
  • 1o6z, 2x0r – HmMDH (mutant)+NAD - Haloarcula marismortui
    
  • 1hlp – HmMDH+NAD
    
  • 1x0i – AfMDH+NADH – Archaeoglobus fulgidus
    
  • 2x0j - AfMDH+etheno-NAD
    
  • 1hlp – HmMDH+NAD
    
  • 1x0i – AfMDH+NADH
    
  • 2x0j - AfMDH+etheno-NAD
    
  • 1ib6, 1ie3 – EcMDH (mutant)+NAD - Escherichia coli
    
  • 3i0p – MDH+NAD – Entamoeba histolytica
    
  • 3gvh – BmMDH+NAD – Brucella melitensis
    
  • 1wze – TfMDH (mutant)+NAD – Thermus flavus
    
  • 1wzi - TfMDH (mutant)+NDP
    
  • 1bmd – TfMDH+NAD
    
  • 1y7t – TtMDH+NADPH – Thermus thermophilus
    
  • 2cvq - TtMDH+NADP
    
  • 1v9n – MDH+NADPH – Pyrococcus horikoshii
    
  • 1z2i – MDH+NAD – Agrobacterium tumefaciens
    
  • 1uxg, 1uxh, 1uxi, 1uxj, 1uxk, 1ur5 – ChaMDH (mutant)+NAD – Chloroflexus aurantiacus
    
  • 1guz, 1guy, 1gv0 – CvMDH+NAD – Chlorobium vibrioforme
    
  • 1civ – MDH+NADP – Flaveria bidentis
    
  • 1b8u, 1b8v – AaMDH+NAD - Aquaspirillum arcticum
    
  • 4i1i – LmMd + NAD – Leishmania major
    
  • 5ujk – MeMd + NAD - Methylobacterium extorquens
    
  • 5nuf, 5nue – AtMd1 + NAD – Arabidopsis thaliana
    
  • 4uup – Md + NADH - Trichiminad
    
  • 5kvv – MtMd + NADH – Mycobacterium tuberculosis
    
  • 6ihd – MsMd + NAD – Metallosphaera sedula
    
  • 6itl – Md + NAD – Mannheimia succiniciproducens
    
  • 6y91 – PfMd + NAD – Plasmodium falciparum
    
  • 6zn7 – BbMd + NADP – Bdellovibrio bacteriovorus
    
  • 7f8d, 7x1l – GsMd (mutant) + NADH – Geobacillus stearophilus
    
  • 8rs5, 9qcg – MkMd + NDP – Methanopyrus kandleri
    
  • 8rwl, 9end – MkMd (mutant) + NDP
    
  • 9sa7 – MjMd + NDP – Methanocaldococcus jannaschii
    
  • 9sc9 – MjMd (mutant) + NDP
    
  • 9sd3 – Md + NDP – Methanocaldococcus infernus
    
  • 9s3k, 9s3y – Md + NDP – ancestral Methanocaldococcus
    
• Md binary complex
  • 7rm9 – hMd1 + malonate
    
  • 4wle – hMd2 + citrate
    
  • 4wlf – hMd2 + malate
    
  • 5kka – EcMd + inhibitor
    
  • 5z3w, 6ka0 – EcMd + Ag
    
  • 9wxs – EcMd (mutant) + Ag
    
  • 2cmd - EcMd + citrate
    
  • 3gvi - BmMDH+ADP
    
  • 2hjr – MDH+adenosine diphosphoribose – Cryptosporidium parvum
    
  • 1bdm - TfMDH (mutant)+beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide
    
  • 6bal – HiMd + malate - Haemophilus influenzae
    
  • 6qss – Md + Tb derivative – Ignicoccus islandicus
    
  • 6zng, 6znt – BbMd + acetyl-CoA
    
  • 6znu – BbMd (mutant) + acetyl-CoA
    
  • 8ggd, 8ggh, 8gh2, 8gh3, 9fef – TcMd + PEX5 – Trypanosoma cruzi – Cryo EM
    
• Md ternary complex
  • 4wlo – hMd2 + NADH + oxaloacetate
    
  • 4wlu – hMd2 + NADH + malate
    
  • 5mdh – pMd+NAD+alpha-ketomalonic acid
    
  • 9d2f – mMd in radial spoke complex – Cryo EM
    
  • 5zi2 – yMd + NAD + ADP - yeast
    
  • 5zi4 – yMd + NAD + oxalacetate
    
  • 4plh, 4plt – ApMd + NAD + oxamate – Apicomplexa
    
  • 4plv, 4plw – ApMd + NAD + lactate
    
  • 4ply – ApMd + NAD + malate
    
  • 4ros – MeMd + oxaloacetate + ADPR
    
  • 1emd – EcMd+NAD+citrate
    
  • 6ihe – MsMd + NAD + malate
    
  • 6itk – Md + NAD + malate – Corynebacterium glutamicum
    
  • 6r8g – PfMd + NAD + thiazol derivative
    
  • 7by9 – GsMd + NADH + oxalacetate – Geobacillus stearophilus
    
  • 7bya – GsMd + adenosine diphosphoribose + oxalacetate
    
  • 8gi0 – TcMd + PEX5 + PEX14 – Cryo EM
    
  • 8xku, 8xkv – AtMd in Ycf2-FtsHI motor complex – Cryo EM
    
  • 8jd5 – AtMd in starch degradation complex – Cryo EM
    
• apo-MDH
  • 7rrl – hMd1
    
  • 4wln – hMd2
    
  • 1mld – pMDH
    
  • 7mdh – MDH – Sorghum
    
  • 5zi3 – yMd
    
  • 2j5r, 2j5k, 2j5q, 1d3a, 4jco – HmMDH
    
  • 2hlp, 7q3x – HmMDH (mutant)
    
  • 3hhp, 2pwz, 6ka1, 7cgc, 7cgd – EcMDH
    
  • 7xqn – EcMd (mutant) br />
  • 3fi9 – MDH – Porphyromonas gingivalis
    
  • 3d5t - MDH – Burkholderia pseudomallei
    
  • 2d4a – MDH – Aeropyrum pernix
    
  • 1iz9, 4kde, 4kdf - TtMDH
    
  • 1sev, 1smk – MDH – Citrullus lanatus
    
  • 1gv1 – CvMDH
    
  • 1b8p – AaMDH
    
  • 3nep – Md – Salinibacter ruber
    
  • 3p7m – Md – Francisella tularensis
    
  • 3tl2 – Md – Bacillus anthracis
    
  • 4e0b – Md – Vibrio vulnificus
    
  • 4h7p - LmMd
    
  • 4cl3 – ChaMd
    
  • 4bgu – Md – Haloferax volcanii
    
  • 4bgv – Md – Picrophilus torridus
    
  • 5ulv – MeMd
    
  • 4tvo – Md – Mycobacterium tuberculosis
    
  • 6aoo – HiMd
    
  • 5nfr – PfMd
    
  • 4uuo – Md – Trichomonas vaginalis
    
  • 6um4 – Md – Naegleria fowleri
    
  • 6pbl – Md – Legionella pneumophila
    
  • 7by8 – GsMd
    
  • 6zn4, 6zn9, 6znj – BbMd
    
  • 6zne, 6znk, 6znr – BbMd (mutant)
    
  • 7aob – Md – Thermaerobacter marianensis
    
  • 7nrz – TcMd
    
  • 9fee – TcMd – Cryo EM
    

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Michal Harel, Joel L. Sussman