SMTL ID : 5uqf.1 (3 other biounits)

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with IMP and the inhibitor P225

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 21 residues within 4Å: Chain A: A.70, M.72, N.194, G.219, S.220, I.221, C.222, D.255, G.256, G.257, M.276, G.278, S.279, Y.302, G.304, M.305, G.306, E.332, G.333 Ligands: 8KY.2, EDO.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.194, A:S.220, A:D.255, A:G.257, A:G.278, A:S.279, A:M.305, A:G.306, A:E.332 IMP.11: 21 residues within 4Å: Chain B: A.70, M.72, N.194, G.219, S.220, I.221, C.222, D.255, G.256, G.257, M.276, G.278, S.279, Y.302, G.304, M.305, G.306, E.332, G.333 Ligands: 8KY.12, EDO.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.194, B:S.220, B:D.255, B:G.257, B:G.278, B:S.279, B:M.305, B:G.306, B:E.332 IMP.21: 21 residues within 4Å: Chain C: A.70, M.72, N.194, G.219, S.220, I.221, C.222, D.255, G.256, G.257, M.276, G.278, S.279, Y.302, G.304, M.305, G.306, E.332, G.333 Ligands: 8KY.22, EDO.27 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.194, C:S.220, C:D.255, C:G.257, C:G.278, C:S.279, C:M.305, C:G.306, C:E.332 IMP.31: 21 residues within 4Å: Chain D: A.70, M.72, N.194, G.219, S.220, I.221, C.222, D.255, G.256, G.257, M.276, G.278, S.279, Y.302, G.304, M.305, G.306, E.332, G.333 Ligands: 8KY.32, EDO.37 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.194, D:S.220, D:D.255, D:G.257, D:G.278, D:S.279, D:M.305, D:G.306, D:E.332

4 x 8KY: {2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenoxy}acetic acid(Non-covalent)

8KY.2: 16 residues within 4Å: Chain A: S.166, A.167, H.168, T.224, M.305, G.306, V.330, E.332 Chain D: V.46, L.47, P.48, S.357, G.360, Y.361 Ligands: IMP.1, EDO.7 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:P.48, D:Y.361, A:A.167 Hydrogen bonds: A:S.166, A:E.332, A:E.332 8KY.12: 16 residues within 4Å: Chain B: S.166, A.167, H.168, T.224, M.305, G.306, V.330, E.332 Chain C: V.46, L.47, P.48, S.357, G.360, Y.361 Ligands: IMP.11, EDO.17 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.167, C:P.48, C:Y.361 Hydrogen bonds: B:S.166, B:E.332, B:E.332 8KY.22: 16 residues within 4Å: Chain A: V.46, L.47, P.48, S.357, G.360, Y.361 Chain C: S.166, A.167, H.168, T.224, M.305, G.306, V.330, E.332 Ligands: IMP.21, EDO.27 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.167, A:P.48, A:Y.361 Hydrogen bonds: C:S.166, C:E.332, C:E.332 8KY.32: 16 residues within 4Å: Chain B: V.46, L.47, P.48, S.357, G.360, Y.361 Chain D: S.166, A.167, H.168, T.224, M.305, G.306, V.330, E.332 Ligands: IMP.31, EDO.37 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:A.167, B:P.48, B:Y.361 Hydrogen bonds: D:S.166, D:E.332, D:E.332

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: G.217, G.219, C.222 Chain D: E.386, S.387, H.388 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Metal complexes: A:G.217, A:G.219, A:C.222, D:E.386, D:S.387 K.13: 6 residues within 4Å: Chain B: G.217, G.219, C.222 Chain C: E.386, S.387, H.388 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:G.217, B:G.219, B:C.222, C:E.386, C:S.387 K.23: 6 residues within 4Å: Chain A: E.386, S.387, H.388 Chain C: G.217, G.219, C.222 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:G.217, C:G.219, C:C.222, A:E.386, A:S.387 K.33: 6 residues within 4Å: Chain B: E.386, S.387, H.388 Chain D: G.217, G.219, C.222 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:G.217, D:G.219, D:C.222, B:E.386, B:S.387

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

SO4.4: 3 residues within 4Å: Chain A: Y.294, Q.295, R.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.294, A:Q.295, A:R.337 SO4.5: 2 residues within 4Å: Chain A: H.78, R.79 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.78 SO4.6: 3 residues within 4Å: Chain A: I.99, Q.147, R.150 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.150 SO4.14: 3 residues within 4Å: Chain B: Y.294, Q.295, R.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.294, B:Q.295, B:R.337 SO4.15: 2 residues within 4Å: Chain B: H.78, R.79 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.78 SO4.16: 3 residues within 4Å: Chain B: I.99, Q.147, R.150 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.150 SO4.24: 3 residues within 4Å: Chain C: Y.294, Q.295, R.337 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.294, C:Q.295, C:R.337 SO4.25: 2 residues within 4Å: Chain C: H.78, R.79 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.78 SO4.26: 3 residues within 4Å: Chain C: I.99, Q.147, R.150 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.150 SO4.34: 3 residues within 4Å: Chain D: Y.294, Q.295, R.337 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.294, D:Q.295, D:R.337 SO4.35: 2 residues within 4Å: Chain D: H.78, R.79 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.78 SO4.36: 3 residues within 4Å: Chain D: I.99, Q.147, R.150 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.150

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 10 residues within 4Å: Chain A: A.167, G.215, I.216, G.217, P.218, C.222, T.224 Chain D: Y.361 Ligands: IMP.1, 8KY.2 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: R.104, R.108 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: R.86 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.297, Y.299, R.337 Chain D: T.393 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain B: A.167, G.215, I.216, G.217, P.218, C.222, T.224 Chain C: Y.361 Ligands: IMP.11, 8KY.12 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: R.104, R.108 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain B: R.86 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.297, Y.299, R.337 Chain C: T.393 Ligand excluded by PLIP EDO.27: 10 residues within 4Å: Chain A: Y.361 Chain C: A.167, G.215, I.216, G.217, P.218, C.222, T.224 Ligands: IMP.21, 8KY.22 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain C: R.104, R.108 Ligand excluded by PLIP EDO.29: 1 residues within 4Å: Chain C: R.86 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: T.393 Chain C: R.297, Y.299, R.337 Ligand excluded by PLIP EDO.37: 10 residues within 4Å: Chain B: Y.361 Chain D: A.167, G.215, I.216, G.217, P.218, C.222, T.224 Ligands: IMP.31, 8KY.32 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain D: R.104, R.108 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain D: R.86 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: T.393 Chain D: R.297, Y.299, R.337 Ligand excluded by PLIP

Links

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Citation

Kim, Y. et al., Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase fromCampylobacter jejuni in the complex with IMP and the inhibitor P225. To Be Published

Release Date

2017-03-01

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Inosine-5'-monophosphate dehydrogenase

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