SMTL ID : 4my9.1 (1 other biounit)

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 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, E.313, G.314 Ligands: C91.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.177, A:S.203, A:S.203, A:D.238, A:G.240, A:G.261, A:S.262, A:S.262, A:M.288, A:G.289, A:E.313 Water bridges: A:G.200, A:G.202, A:G.239, A:G.239, A:S.262, A:S.262, A:M.263 IMP.4: 22 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, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: C91.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: 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:E.313 Water bridges: B:G.239, B:I.241, B:I.241, B:I.241 IMP.8: 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: C91.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:N.177, C:S.203, C:S.203, C:D.238, C:G.240, C:G.261, C:S.262, 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:G.239, C:I.241, C:S.262, C:S.262 IMP.12: 22 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, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: C91.13 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:N.177, D:S.203, D:D.238, 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:I.241, D:I.241, D:S.262

4 x C91: N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide(Non-covalent)

C91.2: 15 residues within 4Å: Chain A: A.150, S.154, T.207, M.288, G.289, M.294, L.310, E.313 Chain C: V.49, L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.1 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.150, A:L.310, C:L.50, C:P.51, C:Y.342 Hydrogen bonds: A:E.313 Water bridges: A:E.313 C91.5: 14 residues within 4Å: Chain A: V.49, P.51, A.338, G.341, Y.342 Chain B: A.150, H.151, S.154, M.288, G.289, M.294, L.310, E.313 Ligands: IMP.4 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.150, B:H.151, B:L.310, A:P.51, A:Y.342 Hydrogen bonds: B:E.313 C91.9: 15 residues within 4Å: Chain C: A.150, H.151, S.154, T.207, M.288, G.289, M.294, L.310, E.313 Chain D: V.49, P.51, A.338, G.341, Y.342 Ligands: IMP.8 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.150, C:L.310, D:P.51, D:A.338, D:Y.342 Hydrogen bonds: C:E.313 C91.13: 15 residues within 4Å: Chain B: V.49, L.50, P.51, A.338, G.341, Y.342 Chain D: A.150, H.151, S.154, T.207, M.288, M.294, L.310, E.313 Ligands: IMP.12 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.50, B:A.338, B:Y.342, D:A.150, D:H.151 Hydrogen bonds: D:E.313

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 5 residues within 4Å: Chain A: E.33, L.35, T.219, Y.222, D.223 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.35 Water bridges: A:E.33, A:E.33 MLI.6: 5 residues within 4Å: Chain B: E.33, L.35, T.219, Y.222, D.223 No protein-ligand interaction detected (PLIP) MLI.7: 9 residues within 4Å: Chain B: S.61, E.62, S.63, R.165, P.169, S.170, L.171, N.172, N.193 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.62, B:S.63, B:N.193 Water bridges: B:S.63 Salt bridges: B:R.165 MLI.10: 9 residues within 4Å: Chain C: S.61, E.62, S.63, R.165, P.169, S.170, L.171, N.172, N.193 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.61, C:E.62, C:E.62, C:S.63, C:L.171 Salt bridges: C:R.165 MLI.11: 7 residues within 4Å: Chain A: F.30 Chain C: E.33, G.34, L.35, T.219, Y.222, D.223 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.219, C:T.219 MLI.14: 4 residues within 4Å: Chain C: F.30 Chain D: E.33, L.35, T.219 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91. To be Published

Release Date

2014-06-11

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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