SMTL ID : 4z0g.2 (1 other biounit)

Structure of the IMPDH from Ashbya gossypii bound to GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 29 residues within 4Å: Chain A: S.77, P.78, M.79, S.170, N.197, R.216, G.220, G.222, S.223, I.224, C.225, T.227, D.258, G.259, G.260, V.261, M.279, M.280, G.281, G.282, Y.305, G.307, M.308, G.309, S.310, Q.339, G.340 Chain C: H.402 Ligands: GOL.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.77, A:N.197, A:R.216, A:S.223, A:S.223, A:T.227, A:D.258, A:D.258, A:G.260, A:G.281, A:G.282, A:Y.305, A:M.308, A:G.309, A:Q.339 Water bridges: A:G.220, A:G.222, A:T.227, A:T.227, A:G.259, A:V.261, A:V.261 5GP.2: 13 residues within 4Å: Chain A: I.147, S.174, V.175, F.176, Q.177 Chain C: I.51, D.52, F.53, P.54, S.55, S.56, H.364, Q.367 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:S.174, A:V.175, A:F.176, C:S.55, C:S.55, C:S.55, C:Q.367 Water bridges: A:S.174, C:D.52, C:S.56 pi-Stacking: A:F.176 pi-Cation interactions: A:F.176 Salt bridges: C:H.364 5GP.5: 29 residues within 4Å: Chain B: S.77, P.78, M.79, S.170, N.197, R.216, G.220, G.222, S.223, I.224, C.225, T.227, D.258, G.259, G.260, V.261, M.279, M.280, G.281, G.282, Y.305, G.307, M.308, G.309, S.310, Q.339, G.340 Chain D: H.402 Ligands: GOL.8 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:S.77, B:N.197, B:R.216, B:S.223, B:S.223, B:T.227, B:D.258, B:D.258, B:G.260, B:G.281, B:G.282, B:Y.305, B:M.308, B:G.309, B:Q.339 Water bridges: B:G.220, B:G.222, B:T.227, B:T.227, B:G.259, B:V.261, B:V.261 5GP.6: 13 residues within 4Å: Chain B: I.147, S.174, V.175, F.176, Q.177 Chain D: I.51, D.52, F.53, P.54, S.55, S.56, H.364, Q.367 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:S.55, D:S.55, D:S.55, D:Q.367, B:S.174, B:V.175, B:F.176 Water bridges: D:D.52, D:S.56, B:S.174 Salt bridges: D:H.364 pi-Stacking: B:F.176 pi-Cation interactions: B:F.176 5GP.9: 29 residues within 4Å: Chain B: H.402 Chain C: S.77, P.78, M.79, S.170, N.197, R.216, G.220, G.222, S.223, I.224, C.225, T.227, D.258, G.259, G.260, V.261, M.279, M.280, G.281, G.282, Y.305, G.307, M.308, G.309, S.310, Q.339, G.340 Ligands: GOL.12 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:S.77, C:N.197, C:R.216, C:S.223, C:S.223, C:T.227, C:D.258, C:D.258, C:G.260, C:G.281, C:G.282, C:Y.305, C:M.308, C:G.309, C:Q.339 Water bridges: C:G.220, C:G.222, C:T.227, C:T.227, C:G.259, C:V.261, C:V.261 5GP.10: 13 residues within 4Å: Chain B: I.51, D.52, F.53, P.54, S.55, S.56, H.364, Q.367 Chain C: I.147, S.174, V.175, F.176, Q.177 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:S.55, B:S.55, B:S.55, B:Q.367, C:S.174, C:V.175, C:F.176 Water bridges: B:D.52, B:S.56, C:S.174 Salt bridges: B:H.364 pi-Stacking: C:F.176 pi-Cation interactions: C:F.176 5GP.13: 29 residues within 4Å: Chain A: H.402 Chain D: S.77, P.78, M.79, S.170, N.197, R.216, G.220, G.222, S.223, I.224, C.225, T.227, D.258, G.259, G.260, V.261, M.279, M.280, G.281, G.282, Y.305, G.307, M.308, G.309, S.310, Q.339, G.340 Ligands: GOL.16 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:S.77, D:N.197, D:R.216, D:S.223, D:S.223, D:T.227, D:D.258, D:D.258, D:G.260, D:G.281, D:G.282, D:Y.305, D:M.308, D:G.309, D:Q.339 Water bridges: D:G.220, D:G.222, D:T.227, D:T.227, D:G.259, D:V.261, D:V.261 5GP.14: 13 residues within 4Å: Chain A: I.51, D.52, F.53, P.54, S.55, S.56, H.364, Q.367 Chain D: I.147, S.174, V.175, F.176, Q.177 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:S.55, A:S.55, A:S.55, A:Q.367, D:S.174, D:V.175, D:F.176 Water bridges: A:D.52, A:S.56, D:S.174 Salt bridges: A:H.364 pi-Stacking: D:F.176 pi-Cation interactions: D:F.176

4 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: G.220, S.221, G.222, C.225 Chain C: E.398, G.399, G.400, H.402 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:E.398, C:G.399, A:G.220, A:G.222, A:C.225 K.7: 8 residues within 4Å: Chain B: G.220, S.221, G.222, C.225 Chain D: E.398, G.399, G.400, H.402 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:E.398, D:G.399, B:G.220, B:G.222, B:C.225 K.11: 8 residues within 4Å: Chain B: E.398, G.399, G.400, H.402 Chain C: G.220, S.221, G.222, C.225 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:G.220, C:G.222, C:C.225, B:E.398, B:G.399 K.15: 8 residues within 4Å: Chain A: E.398, G.399, G.400, H.402 Chain D: G.220, S.221, G.222, C.225 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.398, A:G.399, D:G.220, D:G.222, D:C.225

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: D.168, S.169, S.170, N.197, R.216, M.308, G.309 Ligands: 5GP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.168, A:D.168 Water bridges: A:R.216 GOL.8: 8 residues within 4Å: Chain B: D.168, S.169, S.170, N.197, R.216, M.308, G.309 Ligands: 5GP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.168, B:D.168 Water bridges: B:R.216 GOL.12: 8 residues within 4Å: Chain C: D.168, S.169, S.170, N.197, R.216, M.308, G.309 Ligands: 5GP.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.168, C:D.168 Water bridges: C:R.216 GOL.16: 8 residues within 4Å: Chain D: D.168, S.169, S.170, N.197, R.216, M.308, G.309 Ligands: 5GP.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.168, D:D.168 Water bridges: D:R.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buey, R.M. et al., Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun (2015)

Release Date

2015-11-25

Peptides

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

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