SMTL ID : 5uuv.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with a product IMP and the inhibitor P182

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, M.259, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 8L1.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.177, A:S.203, A:D.238, A:G.240, A:I.241, A:G.261, A:S.262, A:S.262, A:M.288, A:G.289, A:S.290, A:E.313 Water bridges: A:G.202 IMP.5: 22 residues within 4Å: Chain B: A.73, M.75, N.177, P.201, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 8L1.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.177, B:D.238, B:G.240, B:G.261, B:S.262, B:S.262, B:S.262, B:Y.285, B:M.288, B:G.289, B:S.290, B:E.313 IMP.10: 23 residues within 4Å: Chain C: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, M.259, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 8L1.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.238, C:G.240, C:G.261, C:S.262, C:M.288, C:G.289, C:S.290, C:E.313 IMP.13: 22 residues within 4Å: Chain D: A.73, M.75, K.196, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 8L1.14 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.196, D:S.203, D:G.240, D:G.261, D:S.262, D:S.262, D:Y.285, D:M.288, D:G.289, D:S.290, D:E.313 Water bridges: D:S.262, D:S.262

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: 18 residues within 4Å: Chain A: V.126, T.149, A.150, H.151, S.154, V.157, T.207, M.288, G.289, M.294, V.311, E.313 Chain D: L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.1 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:P.51, D:Y.342, A:E.313 Hydrogen bonds: A:T.207, A:T.207, A:E.313, A:E.313 8L1.6: 17 residues within 4Å: Chain B: V.126, T.149, A.150, H.151, S.154, T.207, M.288, G.289, M.294, V.311, E.313 Chain C: L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.5 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:P.51, C:Y.342, B:E.313 Hydrogen bonds: C:Y.342, B:T.207, B:E.313, B:E.313, B:E.313 8L1.11: 17 residues within 4Å: Chain A: L.50, P.51, A.338, G.341, Y.342 Chain C: V.126, T.149, A.150, H.151, S.154, T.207, M.288, G.289, M.294, V.311, E.313 Ligands: IMP.10 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:M.288, C:E.313, A:P.51, A:Y.342 Hydrogen bonds: C:T.207, C:T.207, C:E.313, C:E.313, C:E.313, A:Y.342 8L1.14: 16 residues within 4Å: Chain B: L.50, P.51, A.338, G.341, Y.342 Chain D: V.126, T.149, A.150, H.151, S.154, T.207, M.288, G.289, V.311, E.313 Ligands: IMP.13 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.150, D:M.288, B:Y.342 Hydrogen bonds: D:T.207, D:E.313, D:E.313

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: G.200, G.202, C.205 Chain D: E.367, S.368, H.369 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:G.200, A:C.205, D:E.367 K.4: 6 residues within 4Å: Chain A: E.367, S.368, H.369 Chain C: G.200, G.202, C.205 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:G.200, C:G.202, C:C.205, A:E.367 K.7: 6 residues within 4Å: Chain B: G.200, G.202, C.205 Chain C: E.367, S.368, H.369 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.200, B:G.202, B:C.205 K.9: 6 residues within 4Å: Chain B: E.367, S.368, H.369 Chain D: G.200, G.202, C.205 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:E.367, B:S.368, D:G.202, D:C.205

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain B: R.165, P.169, S.170, L.171, N.172, N.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.171, B:N.193 GOL.12: 7 residues within 4Å: Chain C: S.63, R.165, P.169, S.170, L.171, N.172, N.193 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.63, C:R.165, C:P.169

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 fromBacillus anthracis in the complex with a product IMP and the inhibitor P182. To Be Published

Release Date

2017-03-01

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inosine-5'-monophosphate dehydrogenase

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