SMTL ID : 6mgu.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 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: 22 residues within 4Å: Chain A: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, L.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.292, G.293 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.156, A:T.185, A:T.186, A:G.219, A:G.240, A:S.241, A:Y.264, A:Y.264, A:M.267, A:G.268 Water bridges: A:K.175, A:K.175, A:G.179, A:G.179, A:G.181, A:G.218, A:I.220, A:S.241, A:S.241 JQS.7: 22 residues within 4Å: Chain B: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, L.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.292, G.293 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.156, B:T.185, B:T.186, B:G.219, B:G.240, B:S.241, B:Y.264, B:Y.264, B:M.267, B:G.268 Water bridges: B:K.175, B:K.175, B:G.179, B:G.179, B:G.181, B:G.218, B:I.220, B:S.241, B:S.241 JQS.13: 22 residues within 4Å: Chain C: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, L.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.292, G.293 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:N.156, C:T.185, C:T.186, C:G.219, C:G.240, C:S.241, C:Y.264, C:Y.264, C:M.267, C:G.268 Water bridges: C:K.175, C:K.175, C:G.179, C:G.179, C:G.181, C:G.218, C:I.220, C:S.241, C:S.241 JQS.19: 22 residues within 4Å: Chain D: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, L.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.292, G.293 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:N.156, D:T.185, D:T.186, D:G.219, D:G.240, D:S.241, D:Y.264, D:Y.264, D:M.267, D:G.268 Water bridges: D:K.175, D:K.175, D:G.179, D:G.179, D:G.181, D:G.218, D:I.220, D:S.241, D:S.241

4 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: G.179, P.180, G.181, C.184 Chain C: E.346, S.347, H.348 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:G.179, A:G.181, A:C.184, C:E.346, C:S.347 K.8: 7 residues within 4Å: Chain B: G.179, P.180, G.181, C.184 Chain D: E.346, S.347, H.348 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:G.179, B:G.181, B:C.184, D:E.346, D:S.347 K.14: 7 residues within 4Å: Chain B: E.346, S.347, H.348 Chain C: G.179, P.180, G.181, C.184 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:G.179, C:G.181, C:C.184, B:E.346, B:S.347 K.20: 7 residues within 4Å: Chain A: E.346, S.347, H.348 Chain D: G.179, P.180, G.181, C.184 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.346, A:S.347, D:G.179, D:G.181, D:C.184

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

EDO.3: 5 residues within 4Å: Chain A: E.12, L.14, T.198, Y.201 Chain D: F.9 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: E.12, L.14, T.198, Y.201 Chain C: F.9 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain A: F.9 Chain C: E.12, L.14, T.198, Y.201 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain B: F.9 Chain D: E.12, L.14, T.198, Y.201 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain A: E.41, S.42, R.144, P.148, S.149, N.151, N.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.40 PGE.10: 7 residues within 4Å: Chain B: E.41, S.42, R.144, P.148, S.149, N.151, N.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.40 PGE.16: 7 residues within 4Å: Chain C: E.41, S.42, R.144, P.148, S.149, N.151, N.172 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.40 PGE.22: 7 residues within 4Å: Chain D: E.41, S.42, R.144, P.148, S.149, N.151, N.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.40

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 9 residues within 4Å: Chain A: E.12, G.13, L.14, D.18, R.338, M.339 Chain C: S.340 Ligands: PEG.17, PEG.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.338 Water bridges: A:E.12 PEG.6: 6 residues within 4Å: Chain A: P.30, A.317, G.320, Y.321 Chain D: H.130, E.292 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.292 Water bridges: D:E.292 PEG.11: 9 residues within 4Å: Chain B: E.12, G.13, L.14, D.18, R.338, M.339 Chain D: S.340 Ligands: PEG.17, PEG.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.338 Water bridges: B:E.12 PEG.12: 6 residues within 4Å: Chain B: P.30, A.317, G.320, Y.321 Chain C: H.130, E.292 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.292 Water bridges: C:E.292 PEG.17: 9 residues within 4Å: Chain B: S.340 Chain C: E.12, G.13, L.14, D.18, R.338, M.339 Ligands: PEG.5, PEG.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.338 Water bridges: C:E.12 PEG.18: 6 residues within 4Å: Chain A: H.130, E.292 Chain C: P.30, A.317, G.320, Y.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.292 Water bridges: A:E.292 PEG.23: 9 residues within 4Å: Chain A: S.340 Chain D: E.12, G.13, L.14, D.18, R.338, M.339 Ligands: PEG.5, PEG.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.338 Water bridges: D:E.12 PEG.24: 6 residues within 4Å: Chain B: H.130, E.292 Chain D: P.30, A.317, G.320, Y.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.292 Water bridges: B:E.292

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 Bacillus Anthracis in the complex with inhibitor Oxanosine monophosphate. To Be Published

Release Date

2018-10-24

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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