SMTL ID : 5uqh.2 (1 other biounit)

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor p182

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 8L1.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.194, A:D.255, A:G.257, A:G.278, A:S.279, A:Y.302, A:M.305, A:G.306, A:E.332 Water bridges: A:G.217, A:G.219, A:I.258, A:I.258, A:I.258, A:S.279, A:S.279 IMP.7: 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, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, E.332, G.333 Ligands: 8L1.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.194, 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:G.219, B:S.220, B:G.256, B:I.258, B:I.258, B:L.280 IMP.12: 22 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, I.277, G.278, S.279, Y.302, G.304, M.305, G.306, S.307, E.332, G.333 Ligands: 8L1.13 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.194, C:D.255, C:G.257, C:I.258, C:G.278, C:S.279, C:M.305, C:G.306, C:S.307, C:E.332 Water bridges: C:I.258, C:L.280 IMP.16: 23 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: 8L1.17 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.220, D:D.255, D:G.257, D:G.278, D:S.279, D:M.305, D:G.306, D:S.307, D:E.332 Water bridges: D:G.219, D:G.256, D:I.258, D:I.258, D:I.258, D:S.279, D:S.279

4 x 8L1: N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea(Non-covalent)

8L1.2: 14 residues within 4Å: Chain A: A.167, H.168, T.224, M.305, G.306, M.311, V.330, E.332 Chain B: L.47, P.48, S.357, G.360, Y.361 Ligands: IMP.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.167, A:E.332, B:P.48, B:Y.361 Hydrogen bonds: A:T.224, A:E.332, A:E.332, B:Y.361 8L1.8: 17 residues within 4Å: Chain B: V.145, A.167, H.168, S.171, T.224, M.305, G.306, M.311, V.330, E.332 Chain C: V.46, L.47, P.48, S.357, G.360, Y.361 Ligands: IMP.7 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:P.48, C:Y.361, B:A.167, B:E.332 Hydrogen bonds: C:Y.361, B:T.224, B:E.332, B:E.332 8L1.13: 16 residues within 4Å: Chain C: V.145, S.166, A.167, H.168, S.171, T.224, M.305, G.306, V.330, E.332 Chain D: L.47, P.48, S.357, G.360, Y.361 Ligands: IMP.12 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:P.48, D:Y.361, C:A.167, C:E.332 Hydrogen bonds: D:Y.361, C:T.224, C:E.332, C:E.332, C:E.332 8L1.17: 16 residues within 4Å: Chain A: L.47, P.48, S.357, G.360, Y.361 Chain D: V.145, S.166, A.167, H.168, T.224, M.305, G.306, M.311, V.330, E.332 Ligands: IMP.16 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:P.48, A:Y.361 Hydrogen bonds: A:Y.361, D:T.224, D:E.332, D:E.332 Water bridges: D:E.332

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

EDO.3: 7 residues within 4Å: Chain A: I.53, N.64, M.65, L.87, D.128, L.352, R.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.87, A:R.356 EDO.4: 7 residues within 4Å: Chain A: R.40, P.41, G.42, V.362, R.373, A.374, E.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.375, A:E.375 EDO.9: 6 residues within 4Å: Chain B: I.53, N.64, L.87, D.128, L.352, R.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.87, B:R.356 Water bridges: B:V.51, B:R.356 EDO.10: 7 residues within 4Å: Chain B: R.40, P.41, G.42, V.362, R.373, A.374, E.375 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.40, B:E.375

4 x K: POTASSIUM ION(Non-covalent)

K.5: 7 residues within 4Å: Chain A: E.386, S.387, H.388 Chain D: G.217, P.218, G.219, C.222 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.217, D:G.219, D:C.222, A:E.386, A:S.387 K.6: 6 residues within 4Å: Chain A: G.217, G.219, C.222 Chain B: E.386, S.387, H.388 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.217, A:G.219, A:C.222, B:E.386, B:S.387 K.11: 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.15: 6 residues within 4Å: Chain C: G.217, G.219, C.222 Chain D: E.386, S.387, H.388 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.217, C:G.219, C:C.222, D:E.386, D:S.387

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.14: 4 residues within 4Å: Chain C: I.53, N.64, D.128, R.356 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.53, C:D.128 Hydrogen bonds: C:R.356 Water bridges: C:R.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6. To Be Published

Release Date

2017-03-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

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

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