SMTL ID : 4f7i.2 (1 other biounit)

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x IPM: 3-ISOPROPYLMALIC ACID(Non-covalent)

IPM.1: 13 residues within 4Å: Chain A: L.93, L.94, R.97, R.107, R.135, Y.142, D.244, V.275 Chain B: K.188, V.191, D.220 Ligands: NAD.2, MN.4 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.93, A:L.94, B:V.191 Hydrogen bonds: A:Y.142, B:K.188 Water bridges: A:R.97, A:R.107, A:R.107, A:R.107 Salt bridges: A:R.97, A:R.97, A:R.107, A:R.135, A:R.135, B:K.188, B:K.188 IPM.16: 13 residues within 4Å: Chain A: K.188, V.191, D.220 Chain B: L.93, L.94, R.97, R.107, R.135, Y.142, D.244, V.275 Ligands: NAD.17, MN.19 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.93, B:L.94, A:V.191 Hydrogen bonds: B:Y.142, A:K.188 Water bridges: B:R.97, B:R.97, B:R.107, B:R.107 Salt bridges: B:R.97, B:R.97, B:R.107, B:R.135, B:R.135, A:K.188, A:K.188

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

NAD.2: 29 residues within 4Å: Chain A: I.14, S.74, V.75, G.76, G.77, E.90, L.93, L.257, G.258, E.273, V.275, H.276, G.277, S.278, A.279, P.280, D.281, I.282, A.288, N.289, D.329 Chain B: N.190, Y.218, A.221, H.225 Ligands: IPM.1, K.5, GOL.8, EOH.27 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:N.190, A:V.75, A:G.76, A:E.273, A:H.276, A:G.277, A:G.277, A:S.278, A:A.279, A:D.281, A:N.289 Water bridges: B:H.225, A:A.292, A:D.329 NAD.17: 30 residues within 4Å: Chain A: N.190, Y.218, A.221, M.224, H.225 Chain B: I.14, S.74, V.75, G.76, G.77, E.90, L.93, L.257, G.258, E.273, V.275, H.276, G.277, S.278, A.279, P.280, D.281, I.282, A.288, N.289, D.329 Ligands: IPM.16, K.20, GOL.22, EOH.28 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:N.190, A:Y.218, A:Y.218, B:V.75, B:G.76, B:E.273, B:G.277, B:G.277, B:S.278, B:S.278, B:A.279, B:D.281, B:N.289, B:N.289 Water bridges: A:Q.217, A:H.225, B:R.97, B:A.292 pi-Stacking: B:H.276

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.3: 10 residues within 4Å: Chain A: L.106, P.108, L.132, A.175, K.178, R.179, M.299, E.302, H.303 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.179 Salt bridges: A:K.178, A:E.302, A:H.303 MPO.18: 10 residues within 4Å: Chain B: L.106, P.108, L.132, A.175, K.178, R.179, M.299, E.302, H.303 Ligands: GOL.25 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.179 Water bridges: B:K.178, B:E.302 Salt bridges: B:K.178, B:E.302, B:H.303

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

MN.4: 6 residues within 4Å: Chain A: R.107, D.244, D.248 Chain B: K.188, D.220 Ligands: IPM.1 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.220, A:D.244, H2O.1, H2O.1 MN.19: 6 residues within 4Å: Chain A: K.188, D.220 Chain B: R.107, D.244, D.248 Ligands: IPM.16 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.244, A:D.220, H2O.5, H2O.5

3 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: G.73, S.74, E.273, P.274, H.276 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.73, A:S.74, A:E.273, A:P.274, A:H.276 K.6: 3 residues within 4Å: Chain A: E.65, A.67, T.269 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:A.67, A:T.269, H2O.4 K.20: 6 residues within 4Å: Chain B: G.73, S.74, E.273, P.274, H.276 Ligands: NAD.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.73, B:S.74, B:E.273, B:P.274, B:H.276

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: E.158, Y.160, V.186, V.194, G.195, W.198, T.238, G.239, F.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.158, A:V.186, A:V.194, A:G.239 Water bridges: A:I.241 GOL.8: 10 residues within 4Å: Chain A: G.76, G.77, W.80, D.81, R.88, P.89, E.90 Chain B: Y.218 Ligands: NAD.2, EOH.15 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.77, A:G.77, A:R.88, B:Y.218, B:Y.218 GOL.9: 7 residues within 4Å: Chain A: L.295, A.298, M.299, E.302, E.315 Ligands: MPO.3, GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.298 GOL.10: 11 residues within 4Å: Chain A: P.108, A.109, K.110, F.112, P.254, L.259, L.260, P.261, L.295 Ligands: GOL.9, GOL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.110, A:K.110 GOL.11: 9 residues within 4Å: Chain A: K.110, V.111, F.112, L.115, P.254, L.259, L.295, L.322 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.110, A:F.112, A:L.259 Water bridges: A:L.115 GOL.12: 1 residues within 4Å: Ligands: GOL.13 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain A: I.287, P.328, S.333, G.335 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.333, A:G.335 GOL.21: 9 residues within 4Å: Chain B: E.158, Y.160, V.186, V.194, G.195, W.198, T.238, G.239, F.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.158, B:V.194, B:T.238, B:G.239 Water bridges: B:N.240 GOL.22: 9 residues within 4Å: Chain A: Y.218 Chain B: G.76, G.77, W.80, D.81, R.88, P.89, E.90 Ligands: NAD.17 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.218, A:Y.218, B:G.77, B:G.77, B:R.88 GOL.23: 5 residues within 4Å: Chain A: P.146, W.155 Chain B: P.146, T.157, R.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.159, B:R.159 Water bridges: B:T.157 GOL.24: 7 residues within 4Å: Chain B: K.110, V.111, F.112, L.115, P.254, L.322 Ligands: GOL.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.110, B:F.112 GOL.25: 8 residues within 4Å: Chain B: P.261, L.295, A.298, M.299, E.302, E.315 Ligands: MPO.18, GOL.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.302 GOL.26: 11 residues within 4Å: Chain B: P.108, A.109, K.110, F.112, P.254, L.259, L.260, P.261, L.295 Ligands: GOL.24, GOL.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.110

4 x EOH: ETHANOL(Non-functional Binders)

EOH.14: 4 residues within 4Å: Chain A: S.150, E.151 Chain B: K.162, F.197 No protein-ligand interaction detected (PLIP) EOH.15: 5 residues within 4Å: Chain A: D.81, G.82, L.83, R.88 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.82 Water bridges: A:R.88 EOH.27: 5 residues within 4Å: Chain A: S.256, L.257 Chain B: M.224, R.228 Ligands: NAD.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.228 Hydrophobic interactions: A:L.257 EOH.28: 4 residues within 4Å: Chain A: M.224 Chain B: S.256, L.257 Ligands: NAD.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallo, A. et al., Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. Febs J. (2014)

Release Date

2012-06-13

Peptides

3-isopropylmalate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

3-isopropylmalate dehydrogenase

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