SMTL ID : 4rv8.1

Co-Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum and the inhibitor p131

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 21 residues within 4Å: Chain A: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, E.290, G.291 Ligands: I13.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.51, A:N.152, A:S.178, A:D.213, A:G.215, A:G.236, A:S.237, A:S.237, A:M.263, A:G.264, A:E.290 Water bridges: A:T.182, A:G.214, A:I.216, A:I.216, A:S.237, A:I.238 IMP.5: 22 residues within 4Å: Chain B: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, S.265, E.290, G.291 Ligands: I13.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.51, B:N.152, B:S.178, B:D.213, B:G.215, B:I.216, B:G.236, B:S.237, B:S.237, B:Y.260, B:M.263, B:G.264, B:E.290 Water bridges: B:T.182, B:G.214, B:I.216, B:S.237, B:S.237, B:I.238 IMP.10: 21 residues within 4Å: Chain C: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, E.290, G.291 Ligands: I13.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.51, C:N.152, C:S.178, C:D.213, C:G.215, C:I.216, C:G.236, C:S.237, C:S.237, C:Y.260, C:M.263, C:G.264, C:E.290 Water bridges: C:G.214, C:G.214, C:I.216, C:S.237, C:S.237, C:S.237 IMP.13: 21 residues within 4Å: Chain D: S.51, M.53, N.152, G.177, S.178, I.179, C.180, D.213, G.214, G.215, M.234, I.235, G.236, S.237, Y.260, G.262, M.263, G.264, E.290, G.291 Ligands: I13.12 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.51, D:N.152, D:S.178, D:D.213, D:G.215, D:G.236, D:S.237, D:S.237, D:M.263, D:G.264, D:E.290 Water bridges: D:T.182, D:G.214, D:G.215, D:I.216, D:S.237, D:I.238

4 x I13: 1-(2-{3-[(1E)-N-(2-aminoethoxy)ethanimidoyl]phenyl}propan-2-yl)-3-(4-chloro-3-nitrophenyl)urea(Non-covalent)

I13.2: 17 residues within 4Å: Chain A: S.125, A.126, H.127, N.152, G.173, T.182, M.263, G.264, M.269, V.288, E.290 Chain D: L.28, P.29, S.315, G.318, Y.319 Ligands: IMP.1 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.173, A:E.290, A:E.290 Water bridges: A:N.152, A:G.175, A:T.182, A:T.182, A:T.182, D:S.315, D:S.315 Hydrophobic interactions: D:P.29, D:Y.319 I13.6: 18 residues within 4Å: Chain A: L.28, P.29, S.315, G.318, Y.319 Chain B: S.125, A.126, H.127, N.152, G.173, T.182, M.263, G.264, M.269, V.288, E.290 Ligands: IMP.5, PEG.8 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.29, A:Y.319 Water bridges: A:S.315, A:S.315, B:N.152, B:G.175, B:T.182, B:T.182 Hydrogen bonds: B:G.173, B:E.290, B:E.290 I13.9: 16 residues within 4Å: Chain B: P.29, S.315, G.318, Y.319 Chain C: S.125, A.126, H.127, N.152, G.173, T.182, M.263, G.264, M.269, V.288, E.290 Ligands: IMP.10 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.126, B:P.29, B:Y.319 Hydrogen bonds: C:G.173, C:E.290, C:E.290 Water bridges: C:N.152, C:G.175, C:G.175, C:E.290, C:E.290, B:S.25, B:V.27 I13.12: 16 residues within 4Å: Chain C: L.28, P.29, S.315, G.318, Y.319 Chain D: A.126, H.127, N.152, G.173, T.182, M.263, G.264, M.269, V.288, E.290 Ligands: IMP.13 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:E.290, C:P.29, C:Y.319 Hydrogen bonds: D:N.152, D:G.173, D:E.290, D:E.290 Water bridges: D:A.126, D:G.175, D:G.175, D:T.182, D:T.182, D:E.290, D:E.290, C:S.25, C:V.27

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.41, D.119, I.146, D.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.147, A:D.147 GOL.7: 5 residues within 4Å: Chain B: N.41, V.118, D.119, I.146, D.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.41, B:D.147, B:D.147 GOL.11: 4 residues within 4Å: Chain C: N.41, D.119, I.146, D.147 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.41, C:D.147, C:D.147, C:D.147 GOL.14: 4 residues within 4Å: Chain D: N.23, K.330, K.331, S.332 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: K.286, M.287, V.288 Chain D: P.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.288 PEG.8: 4 residues within 4Å: Chain A: P.29 Chain B: M.287, V.288 Ligands: I13.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity. Acta Crystallogr F Struct Biol Commun (2015)

Release Date

2014-12-31

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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