SMTL ID : 4mz8.1 (1 other biounit)

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with an Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound C91

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: A.70, M.72, N.194, G.219, S.220, I.221, C.222, T.224, D.255, G.256, G.257, M.276, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, S.307, E.332, G.333 Ligands: C91.2 19 PLIP interactions: 19 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:Y.302, A:M.305, A:G.306, A:S.307, A:E.332 Water bridges: A:G.217, A:G.219, A:G.256, A:I.258, A:I.258, A:S.279, A:S.279, A:L.280 IMP.10: 24 residues within 4Å: Chain B: A.70, M.72, N.194, G.219, S.220, I.221, C.222, T.224, D.255, G.256, G.257, M.276, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, S.307, E.332, G.333 Ligands: C91.11, ACY.15 19 PLIP interactions: 19 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:Y.302, B:M.305, B:G.306, B:E.332 Water bridges: B:K.213, B:G.217, B:G.219, B:G.256, B:I.258, B:I.258, B:S.279, B:S.279, B:S.279 IMP.21: 23 residues within 4Å: Chain C: A.70, M.72, N.194, G.219, S.220, I.221, C.222, T.224, D.255, G.256, G.257, M.276, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, S.307, E.332, G.333 Ligands: C91.22 19 PLIP interactions: 19 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:S.307, C:E.332 Water bridges: C:G.217, C:G.219, C:T.224, C:G.256, C:I.258, C:I.258, C:S.279, C:S.279, C:L.280 IMP.30: 24 residues within 4Å: Chain D: A.70, M.72, N.194, G.219, S.220, I.221, C.222, T.224, D.255, G.256, G.257, M.276, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, S.307, E.332, G.333 Ligands: C91.31, ACY.35 19 PLIP interactions: 19 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 Water bridges: D:K.213, D:G.217, D:G.219, D:T.224, D:G.256, D:I.258, D:I.258, D:S.279, D:S.279, D:S.279

4 x C91: N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide(Non-covalent)

C91.2: 13 residues within 4Å: Chain A: A.167, H.168, T.224, M.305, G.306, M.311, E.332 Chain B: V.46, P.48, S.357, G.360, Y.361 Ligands: IMP.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.168, B:P.48, B:Y.361 Hydrogen bonds: A:E.332 Water bridges: A:A.167 C91.11: 16 residues within 4Å: Chain B: A.167, H.168, T.224, M.305, G.306, M.311, L.329, E.332 Chain C: V.46, P.48, S.357, G.360, Y.361 Ligands: IMP.10, ACY.15, EDO.18 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.167, B:H.168, B:L.329, C:P.48, C:Y.361, C:Y.361 Hydrogen bonds: B:E.332 Water bridges: C:S.357 C91.22: 13 residues within 4Å: Chain C: A.167, H.168, T.224, M.305, G.306, M.311, E.332 Chain D: V.46, P.48, S.357, G.360, Y.361 Ligands: IMP.21 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.48, D:Y.361, C:H.168 Hydrogen bonds: C:E.332 Water bridges: C:A.167 C91.31: 16 residues within 4Å: Chain A: V.46, P.48, S.357, G.360, Y.361 Chain D: A.167, H.168, T.224, M.305, G.306, M.311, L.329, E.332 Ligands: IMP.30, ACY.35, EDO.38 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:A.167, D:H.168, D:L.329, A:P.48, A:Y.361, A:Y.361 Hydrogen bonds: D:E.332 Water bridges: D:E.332

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

SO4.3: 4 residues within 4Å: Chain A: R.297, Y.299, R.337 Chain B: T.393 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.393, A:Y.299 Water bridges: B:T.393, B:T.393 Salt bridges: A:R.337 SO4.12: 4 residues within 4Å: Chain B: Y.299, R.337 Chain C: T.393 Ligands: EDO.17 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Y.299, C:T.393, C:T.393 Salt bridges: B:R.337 Water bridges: C:T.393, C:T.393 SO4.14: 1 residues within 4Å: Chain B: R.86 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.86 Salt bridges: B:R.86 SO4.23: 4 residues within 4Å: Chain C: R.297, Y.299, R.337 Chain D: T.393 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:T.393, D:T.393 Salt bridges: C:R.337 SO4.32: 4 residues within 4Å: Chain A: T.393 Chain D: Y.299, R.337 Ligands: EDO.37 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Salt bridges: D:R.337 Hydrogen bonds: A:T.393 Water bridges: A:T.393, A:T.393 SO4.34: 1 residues within 4Å: Chain D: R.86 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.86 Salt bridges: D:R.86

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: S.343, R.345, S.346 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.343 Water bridges: A:S.346 GOL.16: 4 residues within 4Å: Chain B: F.292, Y.294, R.337 Chain C: T.395 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.294, B:R.337, C:T.395 GOL.20: 2 residues within 4Å: Chain B: S.343, R.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.343, B:R.345 GOL.24: 3 residues within 4Å: Chain C: S.343, R.345, S.346 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.343 Water bridges: C:S.346 GOL.36: 4 residues within 4Å: Chain A: T.395 Chain D: F.292, Y.294, R.337 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.294, D:R.337, A:T.395 GOL.40: 2 residues within 4Å: Chain D: S.343, R.345 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.343, D:R.345

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 3 residues within 4Å: Chain A: I.99, Q.147, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.147, A:R.150 FMT.19: 3 residues within 4Å: Chain B: I.99, Q.147, R.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.147, B:R.150 FMT.25: 3 residues within 4Å: Chain C: I.99, Q.147, R.150 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.147, C:R.150 FMT.39: 3 residues within 4Å: Chain D: I.99, Q.147, R.150 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.147, D:R.150

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 5 residues within 4Å: Chain A: I.53, N.64, L.87, D.128, R.356 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.64 Water bridges: A:I.53, A:H.54, A:R.356, A:R.356 Salt bridges: A:R.356 ACY.15: 5 residues within 4Å: Chain B: D.165, S.166, N.194 Ligands: IMP.10, C91.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.165, B:S.166, B:N.194 Salt bridges: B:K.213 ACY.26: 5 residues within 4Å: Chain C: I.53, N.64, L.87, D.128, R.356 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.64 Water bridges: C:I.53, C:H.54, C:R.356, C:R.356 Salt bridges: C:R.356 ACY.35: 5 residues within 4Å: Chain D: D.165, S.166, N.194 Ligands: IMP.30, C91.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.165, D:S.166, D:N.194 Salt bridges: D:K.213

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

EDO.7: 6 residues within 4Å: Chain A: R.86, S.112, E.113, K.131, G.135, L.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.86, A:R.86, A:K.131, A:G.135 EDO.17: 4 residues within 4Å: Chain B: Y.294, Q.295, R.337 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.295, B:R.337 EDO.18: 3 residues within 4Å: Chain B: S.166, A.167 Ligands: C91.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.167 Water bridges: B:K.95 EDO.27: 6 residues within 4Å: Chain C: R.86, S.112, E.113, K.131, G.135, L.137 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.86, C:R.86, C:K.131, C:G.135 EDO.37: 4 residues within 4Å: Chain D: Y.294, Q.295, R.337 Ligands: SO4.32 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.294, D:Q.295, D:R.337 EDO.38: 3 residues within 4Å: Chain D: S.166, A.167 Ligands: C91.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.167 Water bridges: D:K.95

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 5 residues within 4Å: Chain A: T.381 Chain B: T.381 Chain C: T.381 Chain D: T.381 Ligands: CL.28 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: H.170 Chain B: G.42, Y.43 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain A: T.381 Chain B: T.381 Chain C: T.381 Chain D: T.381 Ligands: CL.8 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain C: H.170 Chain D: G.42, Y.43 Ligand excluded by PLIP

2 x 2F2: dimethyl ether(Non-covalent)

2F2.9: 2 residues within 4Å: Chain A: Y.294, Q.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.294, A:Q.295 2F2.29: 2 residues within 4Å: Chain C: Y.294, Q.295 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound C91. To be Published

Release Date

2014-07-16

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Inosine-5'-monophosphate dehydrogenase

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