SMTL ID : 6mgr.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

4 x JQS: 5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid(Non-covalent)

JQS.1: 23 residues within 4Å: Chain A: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: MPD.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.173, A:T.203, A:T.203, A:G.236, A:G.257, A:S.258, A:Y.281, A:Y.281, A:G.283, A:M.284, A:G.285, A:S.286 Water bridges: A:G.196, A:G.198, A:G.235, A:I.237, A:S.258, A:L.259 JQS.11: 23 residues within 4Å: Chain B: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: MPD.20 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.173, B:T.203, B:T.203, B:G.236, B:G.257, B:S.258, B:Y.281, B:Y.281, B:G.283, B:M.284, B:G.285, B:S.286 Water bridges: B:G.198, B:I.237, B:I.237, B:S.258, B:L.259 JQS.22: 23 residues within 4Å: Chain C: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: MPD.29 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.173, C:S.199, C:T.202, C:T.203, C:T.203, C:G.236, C:I.237, C:G.257, C:S.258, C:M.284, C:G.285, C:S.286 Water bridges: C:G.196, C:G.198, C:G.235, C:G.235, C:S.258, C:L.259 JQS.31: 22 residues within 4Å: Chain D: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:N.173, D:S.199, D:S.199, D:S.199, D:T.203, D:T.203, D:G.236, D:G.257, D:S.258, D:M.284, D:G.285 Water bridges: D:G.196, D:G.198, D:G.235, D:I.237, D:S.258, D:L.259

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

SO4.2: 2 residues within 4Å: Chain A: R.65, K.101 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: S.145, A.146, Y.298, F.299, Q.300 Ligands: MPD.8 Ligand excluded by PLIP SO4.12: 8 residues within 4Å: Chain B: K.74, D.144, S.145, A.146, Y.298, F.299, Q.300 Ligands: MPD.20 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: H.57, R.58 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.58, R.65 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: Y.278, R.316 Chain C: T.372 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: S.322, S.325 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain B: R.87 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: S.145, A.146, R.297, Y.298, F.299, Q.300 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: Y.278, R.316 Chain D: T.372 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain C: R.87 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain C: R.65 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain C: S.322, S.325 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: S.145, A.146, Y.298, F.299, Q.300 Ligand excluded by PLIP SO4.33: 1 residues within 4Å: Chain D: H.57 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: N.225, G.228, V.229 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain D: R.83, R.87 Ligand excluded by PLIP

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

CL.4: 4 residues within 4Å: Chain A: T.360 Chain B: T.360 Chain C: T.360 Chain D: T.360 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: I.78, Q.126, R.129 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: S.322 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: N.39, T.41, R.117 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: T.41, R.117 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: Q.126, R.129 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain D: N.39, T.41, R.117 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: I.78, Q.126, R.129 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain D: R.65, K.101 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain D: S.322 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 6 residues within 4Å: Chain A: S.145, A.146, M.284, Q.300 Ligands: JQS.1, SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.284 MPD.20: 6 residues within 4Å: Chain B: A.146, M.284, G.285, Q.300 Ligands: JQS.11, SO4.12 No protein-ligand interaction detected (PLIP) MPD.29: 5 residues within 4Å: Chain C: S.145, A.146, M.284, Q.300 Ligands: JQS.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:M.284

5 x K: POTASSIUM ION(Non-covalent)

K.9: 7 residues within 4Å: Chain A: E.365, S.366, H.367 Chain D: G.196, P.197, G.198, C.201 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.196, D:G.198, D:C.201, A:E.365, A:S.366 K.10: 7 residues within 4Å: Chain A: G.196, P.197, G.198, C.201 Chain B: E.365, S.366, H.367 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.365, B:S.366, A:G.196, A:G.198, A:C.201 K.17: 4 residues within 4Å: Chain B: D.264, S.266, G.268, K.279 No protein-ligand interaction detected (PLIP) K.21: 7 residues within 4Å: Chain B: G.196, P.197, G.198, C.201 Chain C: E.365, S.366, H.367 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:E.365, C:S.366, B:G.196, B:G.198, B:C.201 K.30: 7 residues within 4Å: Chain C: G.196, P.197, G.198, C.201 Chain D: E.365, S.366, H.367 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.196, C:G.198, C:C.201, D:E.365, D:S.366

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 Campylobacter jejuni in the complex with inhibitor Oxanosine Monophosphate. To Be Published

Release Date

2018-10-24

Peptides

Inosine monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inosine monophosphate dehydrogenase

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