SMTL ID : 2d4v.2 (1 other biounit)

Crystal structure of NAD dependent isocitrate dehydrogenase from Acidithiobacillus thiooxidans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 13 residues within 4Å: Chain A: T.105, S.113, N.115, R.119, R.129, R.153, Y.160, D.320 Chain B: K.230, N.232, I.233, D.296 Ligands: NAD.2 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:I.233 Hydrogen bonds: B:K.230, B:K.230, A:N.115, A:Y.160, A:D.320, A:D.320 Water bridges: B:N.232, B:N.232, A:R.129 Salt bridges: B:K.230, A:R.119, A:R.119, A:R.129, A:R.153, A:R.153 FLC.3: 13 residues within 4Å: Chain A: K.230, N.232, I.233, D.296 Chain B: T.105, S.113, N.115, R.119, R.129, R.153, Y.160, D.320 Ligands: NAD.4 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:T.105, B:N.115, B:D.320, B:D.320, A:K.230, A:K.230, A:N.232 Water bridges: B:R.119, B:R.129, B:R.129, A:N.232 Salt bridges: B:R.119, B:R.119, B:R.129, B:R.153, B:R.153, A:K.230 Hydrophobic interactions: A:I.233

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 27 residues within 4Å: Chain A: I.37, K.100, P.102, L.103, E.104, T.105, N.115, R.119, I.333, E.349, T.351, H.352, G.353, T.354, A.355, P.356, D.357, I.358, A.364, N.365, D.405 Chain B: N.232, I.294, N.297, Q.300, Q.301 Ligands: FLC.1 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.100, A:L.103, A:T.105, A:T.105, A:T.105, A:R.119, A:E.349, A:G.353, A:T.354, A:A.355, A:D.357, A:N.365, A:N.365, B:N.232, B:N.297, B:Q.300, B:Q.301 Water bridges: A:I.333, A:S.368, B:N.297 NAD.4: 28 residues within 4Å: Chain A: N.232, I.294, N.297, Q.300, Q.301 Chain B: I.37, K.100, P.102, L.103, E.104, T.105, N.115, R.119, I.333, G.334, E.349, T.351, H.352, G.353, T.354, A.355, P.356, D.357, I.358, A.364, N.365, D.405 Ligands: FLC.3 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.100, B:L.103, B:T.105, B:T.105, B:N.115, B:R.119, B:E.349, B:E.349, B:G.353, B:T.354, B:A.355, B:D.357, B:N.365, B:N.365, A:N.232, A:Q.300, A:Q.301 Water bridges: B:I.333, B:S.368, B:D.405, A:N.297, A:N.297, A:N.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imada, K. et al., Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity. Proteins (2008)

Release Date

2006-11-14

Peptides

isocitrate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

isocitrate dehydrogenase

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