SMTL ID : 4yb4.1

Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.98, D.228, D.232 Chain B: D.204 Ligands: 48Y.2 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.228, B:D.204, H2O.3, H2O.8 MG.4: 5 residues within 4Å: Chain A: D.204 Chain B: R.98, D.228, D.232 Ligands: 48Y.16 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.228, A:D.204, H2O.8, H2O.8 MG.32: 5 residues within 4Å: Chain C: R.98, D.228, D.232 Chain D: D.204 Ligands: 48Y.33 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.228, D:D.204, H2O.13, H2O.14 MG.35: 5 residues within 4Å: Chain C: D.204 Chain D: R.98, D.228, D.232 Ligands: 48Y.54 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.228, C:D.204, H2O.19, H2O.19

4 x 48Y: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid(Non-covalent)

48Y.2: 13 residues within 4Å: Chain A: S.72, R.85, R.88, R.98, R.118, Y.125, D.228 Chain B: K.171, N.173, V.174, D.204 Ligands: MG.1, NAI.3 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.72, A:Y.125, B:K.171, B:N.173 Water bridges: A:R.98, A:R.98, A:R.98 Salt bridges: A:R.85, A:R.88, A:R.88, A:R.98, A:R.118, A:R.118, B:K.171, B:K.171 48Y.16: 14 residues within 4Å: Chain A: K.171, N.173, V.174, D.204 Chain B: S.72, R.85, R.88, R.98, R.118, Y.125, D.228, V.259 Ligands: MG.4, NAI.17 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:K.171, A:N.173, B:S.72, B:Y.125 Salt bridges: A:K.171, B:R.85, B:R.88, B:R.88, B:R.98, B:R.118, B:R.118 Water bridges: B:R.98 48Y.33: 13 residues within 4Å: Chain C: S.72, R.85, R.88, R.98, R.118, Y.125, D.228 Chain D: K.171, N.173, V.174, D.204 Ligands: MG.32, NAI.34 19 PLIP interactions: 13 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:S.72, D:K.171, D:N.173, D:D.204 Water bridges: C:R.88, C:R.98, C:R.98, C:R.98, C:D.232, C:V.259, D:D.204 Salt bridges: C:R.85, C:R.88, C:R.88, C:R.98, C:R.118, C:R.118, D:K.171 Hydrophobic interactions: D:V.174 48Y.54: 13 residues within 4Å: Chain C: K.171, N.173, V.174, D.204 Chain D: S.72, R.85, R.88, R.98, R.118, Y.125, D.228 Ligands: MG.35, NAI.55 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:K.171, C:N.173, D:S.72 Salt bridges: C:K.171, D:R.85, D:R.88, D:R.88, D:R.98, D:R.118, D:R.118 Water bridges: D:R.98, D:D.232, D:D.232

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 27 residues within 4Å: Chain A: I.13, F.67, A.69, A.70, T.71, S.72, I.84, L.241, G.242, E.257, V.259, H.260, G.261, S.262, A.263, P.264, D.265, I.266, A.272, N.273, D.313 Chain B: N.173, I.202, N.205, M.208 Ligands: 48Y.2, GOL.18 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.70, A:S.72, A:E.257, A:G.261, A:G.261, A:S.262, A:A.263, A:D.265, A:N.273, A:N.273, B:N.173, B:N.205 Water bridges: A:R.88, B:N.205, B:Q.209, B:Q.209 NAI.17: 27 residues within 4Å: Chain A: N.173, I.202, N.205, M.208 Chain B: I.13, F.67, A.69, A.70, T.71, S.72, I.84, L.241, G.242, E.257, V.259, H.260, G.261, S.262, A.263, P.264, D.265, I.266, A.272, N.273, D.313 Ligands: GOL.5, 48Y.16 18 PLIP interactions: 3 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:N.173, A:N.205, B:A.70, B:S.72, B:E.257, B:G.261, B:G.261, B:S.262, B:A.263, B:D.265, B:N.273, B:N.273 Water bridges: A:Q.209, B:S.72, B:D.265, B:D.265, B:D.265, B:A.276 NAI.34: 27 residues within 4Å: Chain C: I.13, F.67, A.69, A.70, T.71, S.72, I.84, L.241, G.242, E.257, V.259, H.260, G.261, S.262, A.263, P.264, D.265, I.266, A.272, N.273, D.313 Chain D: N.173, I.202, N.205, M.208 Ligands: 48Y.33, GOL.56 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.70, C:S.72, C:E.257, C:G.261, C:G.261, C:S.262, C:A.263, C:D.265, C:N.273, C:N.273, D:N.173, D:N.205 Water bridges: C:R.88, C:E.257, C:D.265, C:D.313, D:Q.209, D:Q.209 NAI.55: 27 residues within 4Å: Chain C: N.173, I.202, N.205, M.208 Chain D: I.13, F.67, A.69, A.70, T.71, S.72, I.84, L.241, G.242, E.257, V.259, H.260, G.261, S.262, A.263, P.264, D.265, I.266, A.272, N.273, D.313 Ligands: GOL.36, 48Y.54 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:N.173, C:N.205, D:A.70, D:S.72, D:E.257, D:G.261, D:G.261, D:S.262, D:A.263, D:D.265, D:N.273, D:N.273 Water bridges: C:Q.209, D:E.257, D:D.265, D:D.313

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: M.208, M.212, R.213 Chain B: G.240, L.241, D.313 Ligands: NAI.17 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: G.123, L.124, T.178, Q.179, T.223, N.224, L.225 Ligand excluded by PLIP GOL.7: 2 residues within 4Å: Chain A: I.157, R.161 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: P.99, L.279, M.283, E.298 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: G.240, L.241, D.313 Chain B: M.208, M.212, R.213 Ligands: NAI.3 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: G.123, L.124, L.175, Q.179, T.223, N.224, L.225 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: Y.94, A.153, R.156, I.157, I.249 Ligands: GOL.23 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: P.99, R.103, L.279 Ligands: GOL.22 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: V.97, R.161 Ligands: GOL.21, GOL.23 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: V.97, I.249, M.283, D.286, Y.287 Ligands: GOL.20, GOL.22 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain C: M.208, M.212, R.213 Chain D: G.240, L.241, D.313 Ligands: NAI.55 Ligand excluded by PLIP GOL.37: 7 residues within 4Å: Chain C: G.10, H.15, E.38, A.39, E.42, T.43, R.46 Ligand excluded by PLIP GOL.38: 10 residues within 4Å: Chain C: G.123, L.124, A.140, L.175, T.178, Q.179, T.223, N.224, L.225, L.226 Ligand excluded by PLIP GOL.39: 3 residues within 4Å: Chain C: Y.94, R.156, I.249 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain C: I.249, F.256, M.283, D.286, Y.287 Ligands: GOL.41 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain C: P.99, V.115, I.157 Ligands: GOL.40 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain C: P.99, L.279, A.282, M.283, E.298 Ligands: GOL.43 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain C: P.99, A.100, K.101, R.103, V.238, L.243, P.245, L.279 Ligands: GOL.42 Ligand excluded by PLIP GOL.56: 7 residues within 4Å: Chain C: G.240, L.241, D.313 Chain D: M.208, M.212, R.213 Ligands: NAI.34 Ligand excluded by PLIP GOL.57: 6 residues within 4Å: Chain D: G.123, L.124, Q.179, T.223, N.224, L.225 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain D: Y.94, A.153, R.156, I.157, I.249, G.250, D.251 Ligand excluded by PLIP GOL.59: 6 residues within 4Å: Chain D: P.99, R.103, M.283, D.286, E.298 Ligands: GOL.60 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain D: V.97, P.99, I.157, R.161, M.283 Ligands: GOL.59, GOL.61 Ligand excluded by PLIP GOL.61: 6 residues within 4Å: Chain D: V.97, I.249, F.256, M.283, D.286 Ligands: GOL.60 Ligand excluded by PLIP

30 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 2 residues within 4Å: Chain A: R.213, E.215 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: H.170, D.200, I.202 Chain B: T.74 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: P.73, T.74, R.75 Ligands: SO4.15 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: Y.94, A.153, R.156, I.249 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: P.106, R.310 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: Y.94, R.149, R.152, R.156, D.251 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: W.41, T.71, P.73 Ligands: SO4.11 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: R.213, E.215, R.216 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: H.167, Q.209, R.216, F.217 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: P.106, R.310 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: R.163, T.165 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain A: T.74 Chain B: D.200, I.202 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain B: T.49, V.51, P.52, E.53, F.81, Y.86 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: P.309, R.310, G.316, D.317, A.318 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: R.4, E.33, V.35 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain C: R.213, E.215 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain A: L.133 Chain C: T.121, E.122, V.126, V.141 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain C: P.106, R.310 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain C: P.309, R.310, G.316, D.317, A.318 Ligand excluded by PLIP SO4.48: 8 residues within 4Å: Chain C: F.80, F.81, G.82, R.85, E.127 Chain D: N.173, V.174, P.176 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain C: T.49, P.52, E.53 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain C: P.73, T.74, R.75 Ligands: SO4.52 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain C: R.4, E.33, V.35 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain C: W.41, P.73, R.75 Ligands: SO4.50 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain C: D.200, I.202 Chain D: T.74 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain D: R.213, E.215, R.216 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain D: H.167, Q.209, R.216, F.217 Ligand excluded by PLIP SO4.64: 2 residues within 4Å: Chain D: P.106, R.310 Ligand excluded by PLIP SO4.65: 6 residues within 4Å: Chain B: L.133 Chain D: R.89, E.122, V.126, V.141, S.143 Ligand excluded by PLIP SO4.66: 5 residues within 4Å: Chain D: P.309, R.310, G.316, D.317, A.318 Ligand excluded by PLIP

Links

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Citation

Takahashi, K. et al., Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH. To Be Published

Release Date

2016-03-09

Peptides

Homoisocitrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Homoisocitrate dehydrogenase

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