SMTL ID : 1pvn.1

The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x K: POTASSIUM ION(Non-covalent)

K.1: 8 residues within 4Å: Chain A: E.358, G.359, G.360, H.362 Chain D: G.187, G.188, G.189, C.192 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.358, A:G.360, D:G.187, D:G.189, D:C.192 K.2: 6 residues within 4Å: Chain A: D.137, F.139 Chain B: P.18, G.19, S.21, N.333 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.137, A:F.139, B:G.19, B:S.21, B:N.333 K.3: 5 residues within 4Å: Chain A: G.19, S.21, N.333 Chain D: D.137, F.139 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Metal complexes: A:G.19, A:S.21, A:N.333, D:D.137, D:F.139 K.7: 7 residues within 4Å: Chain A: G.187, G.188, G.189, C.192 Chain B: E.358, G.359, G.360 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.358, B:G.359, B:G.360, A:G.189, A:C.192 K.8: 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.12: 6 residues within 4Å: Chain C: D.137, F.139 Chain D: P.18, G.19, S.21, N.333 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:D.137, C:F.139, D:G.19, D:S.21, D:N.333 K.13: 7 residues within 4Å: Chain B: G.187, G.188, G.189, C.192 Chain C: E.358, G.359, G.360 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:G.187, B:G.189, B:C.192, C:E.358, C:G.360 K.16: 8 residues within 4Å: Chain C: G.187, G.188, G.189, C.192 Chain D: E.358, G.359, G.360, H.362 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:G.187, C:G.189, C:C.192, D:E.358, D:G.360

4 x MZP: 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL-IMIDAZOLIUM-5-OLATE-5'-PHOSPHATE(Non-covalent)

MZP.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, R.291, Y.292, E.304, G.305 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: 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:R.291, A:R.291, A:Y.292, A:E.304 Water bridges: A:I.57, A:N.164, A:G.189, A:G.232, A:G.232, A:Y.256 pi-Cation interactions: A:R.291 MZP.9: 21 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, R.291, Y.292, E.304, G.305 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.190, B:D.231, B:G.233, B:G.254, B:R.255, B:E.281, B:G.282, B:S.283, B:R.291, B:R.291, B:Y.292, B:E.304 Water bridges: B:N.164, B:G.189, B:T.194, B:G.232, B:G.232, B:Y.256 pi-Cation interactions: B:R.291 MZP.14: 21 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, R.291, Y.292, E.304, G.305 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:S.190, C:D.231, C:G.233, C:G.254, C:R.255, C:E.281, C:G.282, C:S.283, C:R.291, C:R.291, C:Y.292, C:E.304 Water bridges: C:N.164, C:G.187, C:G.187, C:G.189, C:D.231, C:G.232, C:I.234, C:Y.256 pi-Cation interactions: C:R.291 MZP.17: 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, R.291, Y.292, E.304, G.305 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: 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:S.283, D:R.291, D:Y.292, D:E.304 Water bridges: D:N.164, D:G.187, D:G.189, D:D.231, D:G.232, D:G.232, D:I.234, D:Y.256 pi-Cation interactions: D:R.291

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

TRS.5: 5 residues within 4Å: Chain A: V.212, A.213, N.216 Chain D: A.1, Y.3 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.1, D:A.1, A:V.212, A:N.216 Water bridges: D:A.1 TRS.6: 5 residues within 4Å: Chain A: Y.14, I.209, L.350 Chain D: Y.3, Y.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.14, D:Y.4 Water bridges: A:L.350 TRS.10: 7 residues within 4Å: Chain B: D.237, Y.256, R.259, N.319, A.322, S.323, K.326 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.237, B:R.259, B:R.259 Water bridges: B:N.319, B:N.319 TRS.11: 6 residues within 4Å: Chain A: A.1, Y.3 Chain B: V.212, A.213, N.216, M.246 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.1, A:A.1, A:A.1, B:N.216, B:M.246 Water bridges: A:Y.3, B:A.213 TRS.15: 6 residues within 4Å: Chain B: A.1, Y.3 Chain C: V.212, A.213, N.216, M.246 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:A.1, B:A.1, C:N.216, C:M.246 Water bridges: B:Y.3, C:A.213 TRS.18: 5 residues within 4Å: Chain C: A.1, Y.3 Chain D: V.212, A.213, N.216 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.216, C:A.1, C:A.1 Water bridges: D:A.213, D:R.215, C:A.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, L. et al., The Immunosuppressive Agent Mizoribine Monophosphate Forms a Transition State Analogue Complex with Inosine Monophosphate Dehydrogenase. Biochemistry (2003)

Release Date

2003-07-22

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