SMTL ID : 5uzs.1

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P200

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 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: 8L4.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.154, A:S.180, A:S.180, A:D.215, A:G.217, A:G.238, A:S.239, A:Y.262, A:M.265, A:G.266, A:S.267, A:E.290 Water bridges: A:G.216, A:L.218 IMP.6: 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: 8L4.7 16 PLIP interactions: 16 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:S.180, B:G.216, B:L.218, B:L.218, B:L.218 IMP.13: 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: 8L4.14 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.180, C:D.215, C:G.217, C:G.238, C:S.239, C:M.265, C:G.266, C:S.267, C:E.290 Water bridges: C:G.177, C:G.179, C:L.218, C:L.218, C:L.218, C:L.218, C:I.240 IMP.20: 22 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, E.290, G.291 Ligands: 8L4.21 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.154, D:S.180, D:D.215, D:G.217, D:G.238, D:S.239, D:M.265, D:G.266, D:S.267, D:E.290 Water bridges: D:L.218, D:L.218

4 x 8L4: 3-(2-{[(4-chlorophenyl)carbamoyl]amino}propan-2-yl)-N-hydroxybenzene-1-carboximidamide(Non-covalent)

8L4.2: 15 residues within 4Å: Chain A: A.127, H.128, T.184, M.265, G.266, M.271, F.287, V.288, E.290 Chain C: V.26, P.28, S.315, G.318, Y.319 Ligands: IMP.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.127, A:F.287, C:P.28, C:Y.319 Hydrogen bonds: A:E.290, A:E.290, A:E.290, A:E.290 Halogen bonds: C:V.26 8L4.7: 14 residues within 4Å: Chain A: P.28, S.315, G.318, Y.319 Chain B: A.127, H.128, T.184, M.265, G.266, M.271, F.287, V.288, E.290 Ligands: IMP.6 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.127, B:E.290, A:P.28, A:Y.319 Hydrogen bonds: B:E.290, B:E.290, B:E.290, A:Y.319 Water bridges: B:E.290, A:S.315 8L4.14: 15 residues within 4Å: Chain C: A.127, H.128, T.184, M.265, G.266, M.271, F.287, V.288, E.290 Chain D: V.26, P.28, S.315, G.318, Y.319 Ligands: IMP.13 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.127, C:F.287, C:F.287, D:P.28, D:Y.319 Hydrogen bonds: C:T.184, C:E.290, C:E.290, C:E.290, C:E.290 Halogen bonds: D:V.26 8L4.21: 15 residues within 4Å: Chain B: V.26, P.28, S.315, G.318, Y.319 Chain D: A.127, H.128, T.184, M.265, G.266, M.271, F.287, V.288, E.290 Ligands: IMP.20 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: B:P.28, B:Y.319, D:A.127, D:F.287, D:E.290 Hydrogen bonds: B:Y.319, D:T.184, D:E.290, D:E.290, D:E.290 Halogen bonds: B:V.26 Water bridges: D:E.290, D:E.290

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 4 residues within 4Å: Chain A: L.8, K.9, D.200 Chain C: V.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.9, A:D.200 PGE.4: 5 residues within 4Å: Chain A: N.44, A.65, R.66, E.67, G.68 No protein-ligand interaction detected (PLIP) PGE.10: 4 residues within 4Å: Chain B: L.8, K.9, T.196, D.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.9, B:D.200 PGE.16: 3 residues within 4Å: Chain C: L.8, K.9, D.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.9 PGE.18: 8 residues within 4Å: Chain A: K.286, F.287 Chain C: P.28, N.29, Y.307, I.310, G.311, K.314 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.28, C:K.314

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

PEG.5: 5 residues within 4Å: Chain A: Y.307, I.310, G.311, K.314 Chain B: F.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.314 PEG.8: 5 residues within 4Å: Chain B: N.44, A.65, R.66, E.67, G.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 PEG.15: 5 residues within 4Å: Chain C: N.44, A.65, R.66, E.67, G.68 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.44 PEG.22: 5 residues within 4Å: Chain C: F.287 Chain D: Y.307, I.310, G.311, K.314 No protein-ligand interaction detected (PLIP) PEG.23: 5 residues within 4Å: Chain B: Y.12 Chain D: I.7, L.8, K.9, T.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.10 Water bridges: D:T.10 PEG.24: 5 residues within 4Å: Chain D: N.44, A.65, R.66, E.67, G.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.44

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain A: Y.12 Chain B: I.7, L.8, K.9, T.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.12, B:L.8 EDO.17: 4 residues within 4Å: Chain C: I.7, L.8, K.9, T.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.10, C:T.10

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 2 residues within 4Å: Chain B: E.245, H.301 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.245, B:E.245, B:H.301

2 x K: POTASSIUM ION(Non-covalent)

K.12: 6 residues within 4Å: Chain B: E.344, S.345, H.346 Chain D: G.177, G.179, C.182 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:G.177, D:G.179, D:C.182, B:E.344 K.19: 6 residues within 4Å: Chain C: G.177, G.179, C.182 Chain D: E.344, S.345, H.346 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.177, C:C.182, D:E.344, D:S.345

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.25: 5 residues within 4Å: Chain B: V.20 Chain D: L.8, K.9, T.196, D.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.9, D:D.200

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 P200. To Be Published

Release Date

2017-03-22

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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