SMTL ID : 2y42.1 (1 other biounit)

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

3 x BCN: BICINE(Non-covalent)

BCN.1: 6 residues within 4Å: Chain A: R.107, D.244, D.248 Chain B: D.220, M.224 Ligands: MN.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.107, A:D.244, A:D.248, B:D.220 BCN.4: 7 residues within 4Å: Chain A: D.220, M.224 Chain B: R.107, D.244, D.248 Ligands: NAD.5, MN.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:D.220, B:R.107, B:D.244, B:D.248 Water bridges: B:R.107 BCN.7: 5 residues within 4Å: Chain A: R.228 Chain B: V.252, G.255, S.256, L.257 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.228 Hydrogen bonds: B:V.252, B:G.255, B:L.257 Water bridges: B:G.255

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

NAD.2: 17 residues within 4Å: Chain A: I.14, S.74, G.77, E.90, L.93, L.257, G.258, V.275, H.276, G.277, S.278, A.279, P.280, D.281, I.282, N.289, D.329 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.77, A:V.275, A:G.277, A:S.278, A:A.279, A:D.281, A:N.289, A:N.289 Water bridges: A:E.273, A:E.273 NAD.5: 20 residues within 4Å: Chain B: I.14, S.74, V.75, G.76, G.77, D.81, L.93, G.258, E.273, V.275, H.276, G.277, S.278, A.279, D.281, I.282, A.288, N.289, D.329 Ligands: BCN.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.75, B:E.273, B:G.277, B:G.277, B:S.278, B:A.279, B:D.281, B:N.289, B:N.289 Water bridges: B:A.292

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: D.244, D.248 Chain B: D.220 Ligands: BCN.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.244, A:D.248, B:D.220 MN.6: 4 residues within 4Å: Chain A: D.220 Chain B: D.244, D.248 Ligands: BCN.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.220, B:D.244, B:D.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graczer, E. et al., Atomic Level Description of the Domain Closure in a Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase. Mol.Biosyst. (2011)

Release Date

2011-01-19

Peptides

3-ISOPROPYLMALATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-ISOPROPYLMALATE DEHYDROGENASE

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