SMTL ID : 1xkd.1

Ternary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.287 Chain B: R.136, D.311, D.315 Ligands: ICT.6 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.311, A:D.287, H2O.6, H2O.6 CA.2: 4 residues within 4Å: Chain A: D.311, D.315 Chain B: D.287 Ligands: ICT.4 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.287, A:D.311, H2O.5, H2O.5, H2O.6

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

NAP.3: 19 residues within 4Å: Chain A: K.107, P.109, L.110, T.112, N.122, G.325, E.340, P.341, V.342, H.343, G.344, T.345, A.346, P.347, Y.349, I.355, N.356, D.397, R.400 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.107, A:L.110, A:T.112, A:N.122, A:V.342, A:G.344, A:G.344, A:T.345, A:A.346, A:Y.349, A:Y.349, A:N.356, A:N.356 Salt bridges: A:R.400 NAP.5: 25 residues within 4Å: Chain A: N.235, I.285, N.288, Q.291, Q.292, R.296 Chain B: P.109, L.110, T.112, N.122, R.126, I.324, G.325, E.340, V.342, H.343, G.344, T.345, A.346, K.348, Y.349, I.355, N.356, D.397 Ligands: ICT.6 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:T.112, B:R.126, B:E.340, B:E.340, B:G.344, B:G.344, B:T.345, B:A.346, B:Y.349, B:N.356, B:N.356, A:N.235, A:Q.292, A:Q.292 Salt bridges: B:K.348, A:R.296 Water bridges: A:I.285, A:N.288, A:N.288

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.4: 9 residues within 4Å: Chain A: R.136, R.159, Y.166, D.311 Chain B: K.233, N.235, I.236, D.287 Ligands: CA.2 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.236 Hydrogen bonds: B:K.233, B:N.235 Salt bridges: B:K.233, B:K.233, A:R.136, A:R.159, A:R.159 Water bridges: A:R.136, A:R.136, A:R.136, A:D.315, A:D.315 ICT.6: 16 residues within 4Å: Chain A: K.233, N.235, I.236, D.287 Chain B: T.112, S.120, N.122, V.123, R.126, R.136, R.159, Y.166, D.311, V.342 Ligands: CA.1, NAP.5 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.120, B:N.122, B:Y.166, A:K.233, A:N.235, A:D.287 Water bridges: B:D.315, A:D.287, A:D.287 Salt bridges: B:R.126, B:R.126, B:R.136, B:R.159, B:R.159, A:K.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karlstrom, M. et al., Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. J.Mol.Biol. (2005)

Release Date

2005-10-04

Peptides

isocitrate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

isocitrate dehydrogenase

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