SMTL ID : 1lrt.1

CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 5 residues within 4Å: Chain A: R.114, F.116, W.142 Ligands: BOG.2, TAD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.116, A:W.142 BOG.2: 5 residues within 4Å: Chain A: R.114, D.115, R.117, E.118 Ligands: BOG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117, A:R.117, A:E.118

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: P.18, G.19, S.21, N.333 Chain D: D.137, F.139 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Metal complexes: D:D.137, D:F.139, A:G.19, A:S.21, A:N.333 K.10: 7 residues within 4Å: Chain A: D.137, F.139 Chain B: P.18, G.19, S.21, N.333 Ligands: TRS.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.19, B:S.21, B:N.333, A:D.137, A:F.139 K.16: 6 residues within 4Å: Chain B: D.137, F.139 Chain C: P.18, G.19, S.21, N.333 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:D.137, B:F.139, C:G.19, C:S.21, C:N.333 K.21: 6 residues within 4Å: Chain C: D.137, F.139 Chain D: P.18, G.19, S.21, N.333 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:G.19, D:S.21, D:N.333, C:D.137, C:F.139

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 21 residues within 4Å: Chain A: A.56, M.58, G.189, S.190, I.191, C.192, D.231, G.232, G.233, M.252, L.253, G.254, R.255, Y.278, G.280, E.281, G.282, S.283, E.304, G.305 Ligands: TAD.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.190, A:S.190, A:D.231, A:G.233, A:G.254, A:R.255, A:Y.278, A:E.281, A:G.282, A:S.283, A:E.304 Water bridges: A:N.164, A:K.183, A:G.189, A:G.232, A:I.234, A:Y.256 IMP.11: 19 residues within 4Å: Chain B: A.56, M.58, G.189, S.190, I.191, C.192, D.231, G.232, G.233, M.252, L.253, G.254, R.255, Y.278, G.280, E.281, G.282, S.283 Ligands: TAD.12 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.190, B:S.190, B:D.231, B:G.233, B:G.254, B:R.255, B:E.281, B:G.282 Water bridges: B:N.164, B:K.183, B:G.232, B:I.234, B:I.234, B:Y.256 IMP.17: 19 residues within 4Å: Chain C: A.56, M.58, G.189, S.190, I.191, C.192, D.231, G.232, G.233, M.252, L.253, G.254, R.255, Y.278, G.280, E.281, G.282, S.283 Ligands: TAD.18 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.190, C:S.190, C:D.231, C:G.233, C:G.254, C:R.255, C:E.281, C:G.282, C:S.283 Water bridges: C:K.183, C:G.189, C:G.232, C:G.232, C:I.234, C:Y.256 IMP.22: 21 residues within 4Å: Chain D: A.56, M.58, G.189, S.190, I.191, C.192, D.231, G.232, G.233, M.252, L.253, G.254, R.255, Y.278, G.280, E.281, G.282, S.283, E.304, G.305 Ligands: TAD.23 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.190, D:S.190, D:D.231, D:G.233, D:G.254, D:R.255, D:Y.278, D:E.281, D:G.282, D:E.304 Water bridges: D:N.164, D:G.189, D:D.231, D:G.232, D:I.234, D:I.234, D:I.234, D:Y.256

4 x TAD: BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE(Non-covalent)

TAD.5: 16 residues within 4Å: Chain A: T.113, R.114, D.134, S.135, S.136, W.142, N.164, G.185, I.186, G.187, E.281, G.282, E.304 Ligands: BOG.1, IMP.4, TRS.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.113, A:T.113, A:R.114, A:R.114, A:D.134, A:S.136, A:N.164, A:G.185, A:G.187 Water bridges: A:T.113, A:D.134, A:S.135, A:S.135, A:S.135, A:S.135, A:S.135, A:S.136, A:K.183, A:K.183, A:E.304 pi-Stacking: A:W.142 pi-Cation interactions: A:R.114 TAD.12: 13 residues within 4Å: Chain B: T.113, R.114, D.134, S.135, S.136, W.142, N.164, G.185, I.186, G.187, E.281, G.282 Ligands: IMP.11 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.113, B:T.113, B:R.114, B:R.114, B:D.134, B:S.136, B:N.164, B:G.185, B:G.187 Water bridges: B:D.134, B:D.134, B:S.135, B:D.137, B:K.183, B:K.198, C:C.25 pi-Stacking: B:W.142, B:W.142 pi-Cation interactions: B:R.114 TAD.18: 13 residues within 4Å: Chain C: T.113, R.114, D.134, S.135, S.136, W.142, N.164, G.185, I.186, G.187, E.281, G.282 Ligands: IMP.17 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.113, C:T.113, C:R.114, C:D.134, C:S.136, C:N.164, C:G.185, C:G.187 Water bridges: C:T.113, C:S.135, C:S.135, C:K.183, C:D.231 pi-Stacking: C:W.142 pi-Cation interactions: C:R.114, C:R.114 TAD.23: 15 residues within 4Å: Chain D: T.113, R.114, D.134, S.135, S.136, W.142, N.164, G.185, I.186, G.187, R.195, E.281, G.282, E.304 Ligands: IMP.22 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.113, D:R.114, D:R.114, D:D.134, D:S.136, D:N.164, D:G.185, D:G.187, D:R.195, D:R.195 Water bridges: D:T.113, D:T.113, D:T.113, D:K.183, D:D.231 pi-Stacking: D:W.142, D:W.142, D:W.142 pi-Cation interactions: D:R.114

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 8 residues within 4Å: Chain A: S.135, D.137, S.140, W.142 Chain B: S.21, N.333 Ligands: TAD.5, K.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.21, B:N.333, A:S.135, A:D.137, A:D.137, A:S.140 Water bridges: B:N.333 TRS.7: 6 residues within 4Å: Chain A: K.38, A.175, D.176, G.178, Y.218, I.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.176 Water bridges: A:K.38 TRS.8: 5 residues within 4Å: Chain A: V.212, A.213, N.216 Chain D: A.1, Y.3 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:V.212, A:N.216, D:A.1, D:A.1 Water bridges: D:A.1, D:A.1, D:A.1 TRS.9: 7 residues within 4Å: Chain A: P.35, F.39, Q.43, Q.44, S.45, N.48, P.340 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.43, A:S.45, A:N.48, A:N.48 Water bridges: A:N.48 TRS.13: 7 residues within 4Å: Chain B: D.237, Y.256, R.259, F.260, N.319, A.322, S.323 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.256, B:R.259, B:R.259 Water bridges: B:D.237, B:D.237 TRS.14: 5 residues within 4Å: Chain A: A.1, Y.3 Chain B: V.212, A.213, N.216 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.1, A:A.1, B:N.216 Water bridges: A:Y.3, B:I.209, B:A.213, B:Q.343 TRS.15: 6 residues within 4Å: Chain B: P.35, F.39, Q.43, Q.44, S.45, N.48 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.43, B:Q.44, B:S.45, B:N.48, B:N.48 TRS.19: 6 residues within 4Å: Chain C: D.237, Y.256, R.259, N.319, A.322, S.323 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.237, C:R.259, C:R.259, C:N.319, C:S.323 TRS.20: 5 residues within 4Å: Chain B: A.1, Y.3 Chain C: V.212, A.213, N.216 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:A.1, B:A.1, B:A.1, C:V.212, C:N.216 Water bridges: B:Y.3, C:A.213, C:K.217 TRS.24: 7 residues within 4Å: Chain D: D.237, Y.256, R.259, F.260, N.319, A.322, S.323 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.259, D:R.259, D:N.319 Water bridges: D:D.237, D:D.237 TRS.25: 4 residues within 4Å: Chain C: A.1, Y.3 Chain D: V.212, N.216 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.216, C:A.1, C:A.1 Water bridges: C:A.1, C:A.1 TRS.26: 6 residues within 4Å: Chain D: Y.4, N.5, E.6, P.7, R.202, T.206 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.5, D:N.5, D:P.7 Water bridges: D:R.202, D:D.210

Links

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Citation

Gan, L. et al., Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis. Biochemistry (2003)

Release Date

2003-07-07

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