SMTL ID : 5uze.1

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P182

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 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: 8L1.2 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:S.239, A:M.265, A:G.266, A:E.290 Water bridges: A:G.177, A:G.179, A:G.216, A:G.217, A:L.218, A:S.239, 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: 8L1.5 14 PLIP interactions: 14 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:M.265, B:G.266, B:E.290 Water bridges: B:T.184, B:L.218, B:L.218, B:L.218, B:I.240 IMP.8: 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: 8L1.9 15 PLIP interactions: 15 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:Y.262, C:M.265, C:G.266, C:S.267, C:E.290 Water bridges: C:G.177, C:G.179, C:L.218, C:I.240 IMP.10: 24 residues within 4Å: Chain D: A.50, M.52, N.154, K.173, 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: 8L1.11 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:N.154, D:K.173, D:S.180, D:S.180, D:G.217, D:G.238, D:S.239, D:Y.262, D:M.265, D:G.266, D:E.290 Water bridges: D:T.184, D:L.218, D:L.218, D:L.218, D:I.240

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: 17 residues within 4Å: Chain A: V.103, T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Chain C: V.26, P.28, S.315, G.318, Y.319 Ligands: IMP.1 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:E.290, C:P.28, C:Y.319 Hydrogen bonds: A:T.184, A:T.184, A:E.290, A:E.290, C:Y.319 Halogen bonds: C:V.26 8L1.5: 15 residues within 4Å: Chain A: V.26, P.28, S.315, G.318, Y.319 Chain B: V.103, A.127, H.128, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.4 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.28, A:Y.319, B:A.127, B:E.290 Hydrogen bonds: A:Y.319, B:T.184, B:T.184, B:E.290, B:E.290, B:E.290 Water bridges: A:S.315, A:S.315 8L1.9: 17 residues within 4Å: Chain C: V.103, T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, P.289, E.290 Chain D: P.28, S.315, G.318, Y.319 Ligands: IMP.8 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:E.290, D:P.28, D:Y.319 Hydrogen bonds: C:T.184, C:T.184, C:E.290, C:E.290, D:Y.319 8L1.11: 17 residues within 4Å: Chain B: L.27, P.28, S.315, G.318, Y.319 Chain D: V.103, T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:P.28, B:Y.319 Hydrogen bonds: B:Y.319, D:T.184, D:E.290, D:E.290, D:E.290

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: E.344, S.345, H.346 Chain B: G.177, P.178, G.179, C.182 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.177, B:G.179, B:C.182, A:E.344, A:S.345 K.6: 6 residues within 4Å: Chain B: E.344, S.345, H.346 Chain D: G.177, G.179, C.182 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:G.177, D:G.179, D:C.182, B:E.344, B:S.345

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain B: Y.329, E.330, N.331, A.332 Chain D: R.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.329, B:N.333 Water bridges: B:E.330

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 P182. To Be Published

Release Date

2017-03-22

Peptides

Inosine-5'-monophosphate dehydrogenase,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,Inosine-5'-monophosphate dehydrogenase

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