SMTL ID : 5upv.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis In the presence of G36

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: S.86, M.88, N.191, G.216, S.217, I.218, C.219, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: 8KV.2, EDO.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.86, A:N.191, A:S.217, A:D.252, A:G.254, A:G.275, A:S.276, A:Y.299, A:M.302, A:G.303, A:E.336 Water bridges: A:G.214, A:G.216, A:G.253, A:L.255, A:L.255, A:L.255 IMP.9: 23 residues within 4Å: Chain B: S.86, M.88, N.191, G.216, S.217, I.218, C.219, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: 8KV.10, EDO.15 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.86, B:N.191, B:S.217, B:D.252, B:G.254, B:G.275, B:S.276, B:Y.299, B:M.302, B:G.303, B:E.336 Water bridges: B:G.214, B:G.216, B:G.253, B:L.255, B:L.255, B:L.255 IMP.17: 23 residues within 4Å: Chain C: S.86, M.88, N.191, G.216, S.217, I.218, C.219, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: 8KV.18, EDO.23 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.86, C:N.191, C:S.217, C:D.252, C:G.254, C:G.275, C:S.276, C:Y.299, C:M.302, C:G.303, C:E.336 Water bridges: C:G.214, C:G.216, C:G.253, C:L.255, C:L.255, C:L.255 IMP.25: 23 residues within 4Å: Chain D: S.86, M.88, N.191, G.216, S.217, I.218, C.219, D.252, G.253, G.254, M.273, L.274, G.275, S.276, Y.299, G.301, M.302, G.303, S.304, E.336, G.337 Ligands: 8KV.26, EDO.31 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.86, D:N.191, D:S.217, D:D.252, D:G.254, D:G.275, D:S.276, D:Y.299, D:M.302, D:G.303, D:E.336 Water bridges: D:G.214, D:G.216, D:G.253, D:L.255, D:L.255, D:L.255

4 x 8KV: N-{(1S)-1-[3-methoxy-4-(1,3-oxazol-5-yl)phenyl]ethyl}-N'-phenylurea(Non-covalent)

8KV.2: 14 residues within 4Å: Chain A: A.163, M.302, G.303, M.308, L.333, V.334, E.336 Chain C: P.64, A.361, G.364, Y.365 Ligands: IMP.1, FMT.3, EDO.7 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.163, A:E.336 Hydrogen bonds: A:E.336, A:E.336 Water bridges: A:E.336, A:E.336 pi-Stacking: C:Y.365 8KV.10: 14 residues within 4Å: Chain B: A.163, M.302, G.303, M.308, L.333, V.334, E.336 Chain D: P.64, A.361, G.364, Y.365 Ligands: IMP.9, FMT.11, EDO.15 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B pi-Stacking: D:Y.365 Hydrophobic interactions: B:A.163, B:E.336 Hydrogen bonds: B:E.336, B:E.336 Water bridges: B:E.336, B:E.336 8KV.18: 14 residues within 4Å: Chain B: P.64, A.361, G.364, Y.365 Chain C: A.163, M.302, G.303, M.308, L.333, V.334, E.336 Ligands: IMP.17, FMT.19, EDO.23 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.163, C:E.336 Hydrogen bonds: C:E.336, C:E.336 Water bridges: C:E.336, C:E.336 pi-Stacking: B:Y.365 8KV.26: 14 residues within 4Å: Chain A: P.64, A.361, G.364, Y.365 Chain D: A.163, M.302, G.303, M.308, L.333, V.334, E.336 Ligands: IMP.25, FMT.27, EDO.31 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.163, D:E.336 Hydrogen bonds: D:E.336, D:E.336 Water bridges: D:E.336, D:E.336 pi-Stacking: A:Y.365

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

FMT.3: 3 residues within 4Å: Chain A: T.162, A.163 Ligands: 8KV.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.163 Water bridges: A:H.164 FMT.5: 5 residues within 4Å: Chain A: Q.376, Q.378 Chain D: D.39, H.41, K.42 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.41, A:Q.378 Water bridges: D:K.42 FMT.8: 5 residues within 4Å: Chain A: R.95, A.282, E.283, A.284, P.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.95, A:A.284 FMT.11: 3 residues within 4Å: Chain B: T.162, A.163 Ligands: 8KV.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.163 Water bridges: B:H.164 FMT.13: 5 residues within 4Å: Chain B: Q.376, Q.378 Chain C: D.39, H.41, K.42 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.41, B:Q.378 Water bridges: C:K.42 FMT.16: 5 residues within 4Å: Chain B: R.95, A.282, E.283, A.284, P.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.95, B:A.284 FMT.19: 3 residues within 4Å: Chain C: T.162, A.163 Ligands: 8KV.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.163 Water bridges: C:H.164 FMT.21: 5 residues within 4Å: Chain A: D.39, H.41, K.42 Chain C: Q.376, Q.378 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.41, C:Q.378 Water bridges: A:K.42 FMT.24: 5 residues within 4Å: Chain C: R.95, A.282, E.283, A.284, P.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.95, C:A.284 FMT.27: 3 residues within 4Å: Chain D: T.162, A.163 Ligands: 8KV.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.163 Water bridges: D:H.164 FMT.29: 5 residues within 4Å: Chain B: D.39, H.41, K.42 Chain D: Q.376, Q.378 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.41, D:Q.378 Water bridges: B:K.42 FMT.32: 5 residues within 4Å: Chain D: R.95, A.282, E.283, A.284, P.285 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.95, D:A.284

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

EDO.4: 7 residues within 4Å: Chain A: M.45, A.193, A.229, T.233, A.234, E.237 Chain C: L.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.233 Water bridges: A:A.234 EDO.6: 7 residues within 4Å: Chain A: H.166, N.167, R.168, L.171 Chain C: A.59, S.60, D.61 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.61, A:R.168, A:R.168 EDO.7: 9 residues within 4Å: Chain A: T.162, A.163, N.191, G.212, V.213, G.214, C.219 Ligands: IMP.1, 8KV.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.163, A:N.191, A:G.214 Water bridges: A:T.221 EDO.12: 7 residues within 4Å: Chain B: M.45, A.193, A.229, T.233, A.234, E.237 Chain D: L.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.233 Water bridges: B:A.234 EDO.14: 7 residues within 4Å: Chain B: H.166, N.167, R.168, L.171 Chain D: A.59, S.60, D.61 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.168, B:R.168, D:D.61 EDO.15: 9 residues within 4Å: Chain B: T.162, A.163, N.191, G.212, V.213, G.214, C.219 Ligands: IMP.9, 8KV.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.163, B:N.191, B:G.214 Water bridges: B:T.221 EDO.20: 7 residues within 4Å: Chain B: L.56 Chain C: M.45, A.193, A.229, T.233, A.234, E.237 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.233 Water bridges: C:A.234 EDO.22: 7 residues within 4Å: Chain B: A.59, S.60, D.61 Chain C: H.166, N.167, R.168, L.171 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.61, C:R.168, C:R.168 EDO.23: 9 residues within 4Å: Chain C: T.162, A.163, N.191, G.212, V.213, G.214, C.219 Ligands: IMP.17, 8KV.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.163, C:N.191, C:G.214 Water bridges: C:T.221 EDO.28: 7 residues within 4Å: Chain A: L.56 Chain D: M.45, A.193, A.229, T.233, A.234, E.237 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.233 Water bridges: D:A.234 EDO.30: 7 residues within 4Å: Chain A: A.59, S.60, D.61 Chain D: H.166, N.167, R.168, L.171 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.61, D:R.168, D:R.168 EDO.31: 9 residues within 4Å: Chain D: T.162, A.163, N.191, G.212, V.213, G.214, C.219 Ligands: IMP.25, 8KV.26 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.163, D:N.191, D:G.214 Water bridges: D:T.221

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 G36. To Be Published

Release Date

2017-02-22

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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