SMTL ID : 5vsv.1

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P225

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8KY.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.154, A:S.180, A:D.215, A:G.217, A:G.238, A:S.239, A:M.265, A:G.266, A:E.290 Water bridges: A:K.173, A:G.177, A:G.179, A:T.184, A:G.216, A:G.216, A:L.218, A:I.240 IMP.4: 23 residues within 4Å: Chain B: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8KY.3 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.154, B:S.180, B:D.215, B:G.217, B:G.238, B:S.239, B:Y.262, B:M.265, B:G.266, B:S.267, B:E.290 Water bridges: B:K.173, B:G.177, B:G.179, B:S.180, B:G.216, B:L.218, B:L.218 IMP.6: 23 residues within 4Å: Chain C: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8KY.7 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:N.154, C:S.180, C:D.215, C:G.217, C:G.238, C:S.239, C:M.265, C:G.266, C:E.290 Water bridges: C:G.216, C:G.216, C:L.218, C:L.218, C:I.240 IMP.8: 23 residues within 4Å: Chain D: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8KY.5 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:N.154, D:K.173, D:K.173, D:S.180, D:G.217, D:G.238, D:S.239, D:Y.262, D:M.265, D:G.266, D:S.267, D:E.290 Water bridges: D:G.177, D:G.179, D:S.180, D:T.184, D:G.216, D:L.218, D:L.218, D:L.218

4 x 8KY: {2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenoxy}acetic acid(Non-covalent)

8KY.2: 16 residues within 4Å: Chain A: T.126, A.127, H.128, T.184, M.265, G.266, M.271, V.288, P.289, E.290 Chain C: L.27, P.28, S.315, G.318, Y.319 Ligands: IMP.1 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:A.127, A:E.290, C:P.28, C:Y.319 Hydrogen bonds: A:A.127, A:H.128, A:E.290, A:E.290 Water bridges: A:S.131, C:S.315, C:S.315 8KY.3: 15 residues within 4Å: Chain A: V.26, P.28, S.315, G.318, Y.319 Chain B: T.126, A.127, H.128, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.127, B:E.290, B:E.290 Hydrophobic interactions: A:P.28, A:Y.319 8KY.5: 15 residues within 4Å: Chain B: L.27, P.28, S.315, G.318, Y.319 Chain D: T.126, A.127, H.128, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.8 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:P.28, B:Y.319, D:E.290 Hydrogen bonds: D:A.127, D:H.128, D:E.290, D:E.290 Water bridges: D:S.131 8KY.7: 15 residues within 4Å: Chain C: T.126, A.127, H.128, T.184, M.265, G.266, M.271, V.288, E.290 Chain D: V.26, P.28, S.315, G.318, Y.319 Ligands: IMP.6 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.127, C:H.128, C:E.290, C:E.290 Hydrophobic interactions: D:P.28, D:Y.319 Halogen bonds: D:V.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Inosine 5'-monophosphate Dehydrogenase fromClostridium perfringens Complexed with IMP and P225. To Be Published

Release Date

2017-05-24

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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