SMTL ID : 4aou.1

CtIDH bound to NADP. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 14 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.273, A.305 Chain B: K.210, I.213, D.250 Ligands: MG.2, NAP.3 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, B:K.210, B:D.250 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.210, B:K.210 Water bridges: B:D.250 ICT.4: 14 residues within 4Å: Chain A: K.210, I.213, D.250 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.273, A.305 Ligands: MG.5, NAP.6 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:Y.139, A:K.210, A:D.250 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.210, A:K.210

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.273 Chain B: D.250 Ligands: ICT.1 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.273, B:D.250, H2O.2 MG.5: 3 residues within 4Å: Chain A: D.250 Chain B: D.273 Ligands: ICT.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.250, B:D.273, H2O.3

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 22 residues within 4Å: Chain A: K.72, A.74, T.75, T.77, R.82, N.96, L.286, A.287, H.306, G.307, T.308, V.309, T.310, R.311, H.312, T.324, N.325, D.372 Chain B: L.248, D.251, R.255 Ligands: ICT.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:G.307, A:G.307, A:T.308, A:V.309, A:N.325, A:N.325, B:R.255 Water bridges: A:T.75, A:A.328 Salt bridges: A:H.312, B:R.255 NAP.6: 22 residues within 4Å: Chain A: L.248, D.251, R.255 Chain B: K.72, A.74, T.75, T.77, R.82, N.96, L.286, A.287, H.306, G.307, T.308, V.309, T.310, R.311, H.312, T.324, N.325, D.372 Ligands: ICT.4 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:R.255, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.307, B:G.307, B:T.308, B:V.309, B:N.325, B:N.325 Salt bridges: A:R.255, B:H.312 Water bridges: B:A.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leiros, H.K. et al., The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism. Febs Open Bio (2012)

Release Date

2012-07-11

Peptides

ISOCITRATE DEHYDROGENASE [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ISOCITRATE DEHYDROGENASE [NADP]

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