SMTL ID : 2y3z.1

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 6 residues within 4Å: Chain A: R.107, R.135, D.244, D.248 Chain B: D.220 Ligands: 2PE.3 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.107, A:R.135, A:D.244, B:D.220 Water bridges: A:R.135, A:D.244, A:S.247, A:D.248, B:K.188, B:K.188, B:N.190, B:D.220 TRS.8: 6 residues within 4Å: Chain A: D.220 Chain B: R.107, R.135, D.244, D.248 Ligands: 2PE.10 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Water bridges: A:K.188, A:K.188, A:N.190, A:D.220, B:R.135, B:S.247, B:D.248 Hydrogen bonds: B:R.107, B:R.135, B:D.244

6 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.2: 9 residues within 4Å: Chain A: V.171, E.174, A.175, K.178, L.265, H.303, A.304, F.305, G.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.178, A:H.303 Water bridges: A:E.174 2PE.3: 11 residues within 4Å: Chain A: R.97, N.105, R.135, L.137, Y.142, F.143, S.262, E.273 Chain B: V.191 Ligands: TRS.1, GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:S.262 2PE.4: 12 residues within 4Å: Chain A: V.75, G.76, G.77, L.257, H.276, G.277, S.278, A.279, P.280, A.288, N.289 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.75, A:G.277, A:S.278, A:A.279, A:N.289, A:N.289 2PE.9: 9 residues within 4Å: Chain B: V.171, E.174, A.175, K.178, L.265, H.303, A.304, F.305, G.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.178, B:H.303 2PE.10: 11 residues within 4Å: Chain A: V.191 Chain B: R.97, N.105, R.135, L.137, Y.142, F.143, S.262, E.273 Ligands: TRS.8, GOL.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.135, B:R.135, B:S.262 Water bridges: B:Y.142 2PE.11: 12 residues within 4Å: Chain B: V.75, G.76, G.77, L.257, H.276, G.277, S.278, A.279, P.280, A.288, N.289 Ligands: GOL.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.75, B:G.277, B:S.278, B:A.279, B:N.289, B:N.289

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: K.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.79 GOL.6: 3 residues within 4Å: Chain A: Q.217, R.232, F.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:R.232 GOL.7: 9 residues within 4Å: Chain A: S.74, V.75, E.273, P.274, V.275, H.276, G.277 Ligands: 2PE.3, 2PE.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.75, A:V.75, A:E.273, A:V.275 GOL.12: 1 residues within 4Å: Chain B: K.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.79 GOL.13: 3 residues within 4Å: Chain B: Q.217, R.232, F.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.217, B:R.232 GOL.14: 9 residues within 4Å: Chain B: S.74, V.75, E.273, P.274, V.275, H.276, G.277 Ligands: 2PE.10, 2PE.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.75, B:V.75, B:E.273, B:E.273, B:V.275

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
A

3-ISOPROPYLMALATE DEHYDROGENASE

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