SMTL ID : 5uuw.1 (1 other biounit)

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Bacillus anthracis in the complex with IMP and the inhibitor P221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 21 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, G.261, S.262, Y.285, G.287, M.288, G.289, E.313, G.314 Ligands: 8N1.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.177, A:S.203, A:S.203, A:S.203, A:D.238, A:G.240, A:G.261, A:S.262, A:M.288, A:G.289, A:S.290, A:E.313 Water bridges: A:G.200, A:G.202, A:T.207 IMP.8: 23 residues within 4Å: Chain B: 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: 8N1.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.177, B:S.203, B:S.203, B:D.238, B:G.240, B:G.261, B:S.262, B:M.288, B:G.289, B:S.290, B:E.313 Water bridges: B:G.200, B:G.202, B:T.207, B:G.239, B:G.239 IMP.11: 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: 8N1.12 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.177, C:S.203, C:D.238, C:G.240, C:G.261, C:S.262, C:Y.285, C:M.288, C:G.289, C:S.290, C:E.313 Water bridges: C:G.200, C:G.202, C:S.203, C:G.239, C:G.239, C:I.241 IMP.15: 23 residues within 4Å: Chain D: 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: 8N1.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:N.177, D:K.196, D:S.203, D:G.240, D:G.261, D:S.262, D:Y.285, D:M.288, D:G.289, D:S.290, D:E.313 Water bridges: D:G.74, D:G.239

4 x 8N1: N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine(Non-covalent)

8N1.2: 19 residues within 4Å: Chain A: V.126, T.149, A.150, H.151, S.154, V.157, T.207, M.288, G.289, V.311, P.312, E.313 Chain C: L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.1, GOL.6 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:P.51, C:Y.342, A:A.150, A:E.313 Hydrogen bonds: A:T.149, A:H.151, A:S.154, A:E.313, A:E.313 8N1.9: 18 residues within 4Å: Chain A: L.50, P.51, A.338, G.341, Y.342 Chain B: V.126, T.149, A.150, H.151, S.154, V.157, T.207, M.288, G.289, M.294, V.311, E.313 Ligands: IMP.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.150, B:E.313, A:P.51, A:Y.342 Hydrogen bonds: B:T.149, B:H.151, B:H.151, B:S.154, B:S.154, B:E.313, B:E.313 8N1.12: 18 residues within 4Å: Chain C: T.149, A.150, H.151, S.154, V.157, T.207, M.288, G.289, M.294, V.311, E.313 Chain D: S.47, L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.11 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:P.51, D:A.338, D:Y.342, C:A.150, C:E.313 Halogen bonds: D:S.47 Hydrogen bonds: C:S.154, C:S.154, C:S.154, C:E.313, C:E.313 8N1.16: 17 residues within 4Å: Chain B: L.50, P.51, A.338, G.341, Y.342 Chain D: T.149, A.150, H.151, S.154, V.157, T.207, M.288, G.289, M.294, V.311, E.313 Ligands: IMP.15 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.150, D:E.313, B:P.51, B:A.338, B:Y.342 Hydrogen bonds: D:H.151, D:S.154, D:E.313, D:E.313

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: V.59, G.232, H.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.59, A:G.232 GOL.4: 3 residues within 4Å: Chain A: V.373, Q.374, I.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.374, A:I.375 GOL.6: 3 residues within 4Å: Chain A: L.310, V.311 Ligands: 8N1.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.311 GOL.13: 4 residues within 4Å: Chain C: I.68, H.330, V.333, R.337 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.90, C:H.330, C:R.337, C:R.337

4 x K: POTASSIUM ION(Non-covalent)

K.5: 7 residues within 4Å: Chain A: E.367, S.368, H.369 Chain B: G.200, P.201, G.202, C.205 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.200, B:G.202, B:C.205, A:E.367, A:S.368 K.7: 7 residues within 4Å: Chain A: G.200, P.201, G.202, C.205 Chain C: E.367, S.368, H.369 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:E.367, C:S.368, A:G.200, A:G.202, A:C.205 K.10: 7 residues within 4Å: Chain B: E.367, S.368, H.369 Chain D: G.200, P.201, G.202, C.205 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:G.200, D:G.202, D:C.205, B:E.367, B:S.368 K.14: 7 residues within 4Å: Chain C: G.200, P.201, G.202, C.205 Chain D: E.367, S.368, H.369 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.200, C:G.202, C:C.205, D:E.367, D:S.368

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 IMP and the inhibitor P221. To Be Published

Release Date

2017-03-08

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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