SMTL ID : 6rpu.1

Structure of the ternary complex of the IMPDH enzyme from Ashbya gossypii bound to the dinucleoside polyphosphate Ap5G and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-octamer

Ligands

8 x G5P: P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE(Non-covalent)

G5P.1: 34 residues within 4Å: Chain A: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 Chain E: R.167, K.207 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.115, A:N.118, A:V.125, A:A.146, A:G.147, A:G.147, A:G.147, A:T.165, A:S.166, A:S.166, A:R.167, A:D.168, A:D.168, A:T.184, A:I.188, A:K.208, A:G.209, A:K.210, A:K.210, A:S.225, A:T.227, A:D.228, A:D.228, A:K.231 Salt bridges: A:K.210, A:K.210, A:K.210, A:K.210, E:R.167 pi-Stacking: A:F.145, A:F.145 pi-Cation interactions: A:F.145 G5P.7: 34 residues within 4Å: Chain B: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 Chain F: R.167, K.207 32 PLIP interactions: 31 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:K.115, B:N.118, B:V.125, B:A.146, B:G.147, B:G.147, B:G.147, B:T.165, B:S.166, B:S.166, B:R.167, B:D.168, B:D.168, B:T.184, B:I.188, B:K.208, B:G.209, B:K.210, B:K.210, B:S.225, B:T.227, B:D.228, B:D.228, B:K.231 Salt bridges: B:K.210, B:K.210, B:K.210, B:K.210, F:R.167 pi-Stacking: B:F.145, B:F.145 pi-Cation interactions: B:F.145 G5P.13: 34 residues within 4Å: Chain C: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 Chain H: R.167, K.207 32 PLIP interactions: 31 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:K.115, C:N.118, C:V.125, C:A.146, C:G.147, C:G.147, C:G.147, C:T.165, C:S.166, C:S.166, C:R.167, C:D.168, C:D.168, C:T.184, C:I.188, C:K.208, C:G.209, C:K.210, C:K.210, C:S.225, C:T.227, C:D.228, C:D.228, C:K.231 Salt bridges: C:K.210, C:K.210, C:K.210, C:K.210, H:R.167 pi-Stacking: C:F.145, C:F.145 pi-Cation interactions: C:F.145 G5P.19: 34 residues within 4Å: Chain D: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 Chain G: R.167, K.207 32 PLIP interactions: 31 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:K.115, D:N.118, D:V.125, D:A.146, D:G.147, D:G.147, D:G.147, D:T.165, D:S.166, D:S.166, D:R.167, D:D.168, D:D.168, D:T.184, D:I.188, D:K.208, D:G.209, D:K.210, D:K.210, D:S.225, D:T.227, D:D.228, D:D.228, D:K.231 Salt bridges: D:K.210, D:K.210, D:K.210, D:K.210, G:R.167 pi-Stacking: D:F.145, D:F.145 pi-Cation interactions: D:F.145 G5P.25: 34 residues within 4Å: Chain A: R.167, K.207 Chain E: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 32 PLIP interactions: 31 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.115, E:N.118, E:V.125, E:A.146, E:G.147, E:G.147, E:G.147, E:T.165, E:S.166, E:S.166, E:R.167, E:D.168, E:D.168, E:T.184, E:I.188, E:K.208, E:G.209, E:K.210, E:K.210, E:S.225, E:T.227, E:D.228, E:D.228, E:K.231 Salt bridges: E:K.210, E:K.210, E:K.210, E:K.210, A:R.167 pi-Stacking: E:F.145, E:F.145 pi-Cation interactions: E:F.145 G5P.31: 34 residues within 4Å: Chain B: R.167, K.207 Chain F: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 32 PLIP interactions: 31 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:K.115, F:N.118, F:V.125, F:A.146, F:G.147, F:G.147, F:G.147, F:T.165, F:S.166, F:S.166, F:R.167, F:D.168, F:D.168, F:T.184, F:I.188, F:K.208, F:G.209, F:K.210, F:K.210, F:S.225, F:T.227, F:D.228, F:D.228, F:K.231 Salt bridges: F:K.210, F:K.210, F:K.210, F:K.210, B:R.167 pi-Stacking: F:F.145, F:F.145 pi-Cation interactions: F:F.145 G5P.37: 34 residues within 4Å: Chain D: R.167, K.207 Chain G: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 32 PLIP interactions: 1 interactions with chain D, 31 interactions with chain G Salt bridges: D:R.167, G:K.210, G:K.210, G:K.210, G:K.210 Hydrogen bonds: G:K.115, G:N.118, G:V.125, G:A.146, G:G.147, G:G.147, G:G.147, G:T.165, G:S.166, G:S.166, G:R.167, G:D.168, G:D.168, G:T.184, G:I.188, G:K.208, G:G.209, G:K.210, G:K.210, G:S.225, G:T.227, G:D.228, G:D.228, G:K.231 pi-Stacking: G:F.145, G:F.145 pi-Cation interactions: G:F.145 G5P.43: 34 residues within 4Å: Chain C: R.167, K.207 Chain H: K.115, Y.116, E.117, N.118, I.121, P.124, V.125, K.140, F.145, A.146, G.147, F.148, I.163, I.164, T.165, S.166, R.167, D.168, T.184, D.186, V.187, I.188, K.208, G.209, K.210, L.211, P.212, M.223, S.225, T.227, D.228, K.231 32 PLIP interactions: 31 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:K.115, H:N.118, H:V.125, H:A.146, H:G.147, H:G.147, H:G.147, H:T.165, H:S.166, H:S.166, H:R.167, H:D.168, H:D.168, H:T.184, H:I.188, H:K.208, H:G.209, H:K.210, H:K.210, H:S.225, H:T.227, H:D.228, H:D.228, H:K.231 Salt bridges: H:K.210, H:K.210, H:K.210, H:K.210, C:R.167 pi-Stacking: H:F.145, H:F.145 pi-Cation interactions: H:F.145

8 x GDP: GUANOSINE-5'-DIPHOSPHATE(Covalent)

GDP.2: 13 residues within 4Å: Chain A: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.118, A:N.200, A:N.200, A:N.232, A:K.240, A:K.245 Salt bridges: A:K.240, A:K.245, A:K.245 GDP.8: 13 residues within 4Å: Chain B: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.118, B:N.200, B:N.200, B:N.232, B:K.240, B:K.245 Salt bridges: B:K.240, B:K.245, B:K.245 GDP.14: 13 residues within 4Å: Chain C: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.118, C:N.200, C:N.200, C:N.232, C:K.240, C:K.245 Salt bridges: C:K.240, C:K.245, C:K.245 GDP.20: 13 residues within 4Å: Chain D: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.118, D:N.200, D:N.200, D:N.232, D:K.240, D:K.245 Salt bridges: D:K.240, D:K.245, D:K.245 GDP.26: 13 residues within 4Å: Chain E: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:E.117, E:N.118, E:N.200, E:N.200, E:N.232, E:K.240, E:K.245 Salt bridges: E:K.240, E:K.245, E:K.245 GDP.32: 13 residues within 4Å: Chain F: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:E.117, F:N.118, F:N.200, F:N.200, F:N.232, F:K.240, F:K.245 Salt bridges: F:K.240, F:K.245, F:K.245 GDP.38: 13 residues within 4Å: Chain G: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:E.117, G:N.118, G:N.200, G:N.200, G:N.232, G:K.240, G:K.245 Salt bridges: G:K.240, G:K.245, G:K.245 GDP.44: 13 residues within 4Å: Chain H: E.117, N.118, G.119, L.196, N.200, K.204, L.224, S.225, D.228, L.229, N.232, K.240, K.245 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:E.117, H:N.118, H:N.200, H:N.200, H:N.232, H:K.240, H:K.245 Salt bridges: H:K.240, H:K.245, H:K.245

32 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 9 residues within 4Å: Chain A: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.4: 4 residues within 4Å: Chain A: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.5: 1 residues within 4Å: Chain A: S.234 Ligand excluded by PLIP ACT.6: 3 residues within 4Å: Chain A: K.19, K.489, S.494 Ligand excluded by PLIP ACT.9: 9 residues within 4Å: Chain B: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.10: 4 residues within 4Å: Chain B: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.11: 1 residues within 4Å: Chain B: S.234 Ligand excluded by PLIP ACT.12: 3 residues within 4Å: Chain B: K.19, K.489, S.494 Ligand excluded by PLIP ACT.15: 9 residues within 4Å: Chain C: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.16: 4 residues within 4Å: Chain C: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.17: 1 residues within 4Å: Chain C: S.234 Ligand excluded by PLIP ACT.18: 3 residues within 4Å: Chain C: K.19, K.489, S.494 Ligand excluded by PLIP ACT.21: 9 residues within 4Å: Chain D: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.22: 4 residues within 4Å: Chain D: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.23: 1 residues within 4Å: Chain D: S.234 Ligand excluded by PLIP ACT.24: 3 residues within 4Å: Chain D: K.19, K.489, S.494 Ligand excluded by PLIP ACT.27: 9 residues within 4Å: Chain E: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.28: 4 residues within 4Å: Chain E: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.29: 1 residues within 4Å: Chain E: S.234 Ligand excluded by PLIP ACT.30: 3 residues within 4Å: Chain E: K.19, K.489, S.494 Ligand excluded by PLIP ACT.33: 9 residues within 4Å: Chain F: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.34: 4 residues within 4Å: Chain F: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.35: 1 residues within 4Å: Chain F: S.234 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain F: K.19, K.489, S.494 Ligand excluded by PLIP ACT.39: 9 residues within 4Å: Chain G: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.40: 4 residues within 4Å: Chain G: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.41: 1 residues within 4Å: Chain G: S.234 Ligand excluded by PLIP ACT.42: 3 residues within 4Å: Chain G: K.19, K.489, S.494 Ligand excluded by PLIP ACT.45: 9 residues within 4Å: Chain H: S.74, D.367, G.368, G.369, V.370, M.388, M.389, G.390, G.391 Ligand excluded by PLIP ACT.46: 4 residues within 4Å: Chain H: D.277, S.278, S.279, Q.280 Ligand excluded by PLIP ACT.47: 1 residues within 4Å: Chain H: S.234 Ligand excluded by PLIP ACT.48: 3 residues within 4Å: Chain H: K.19, K.489, S.494 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Justel, D. et al., The Bateman domain of IMP dehydrogenase is a binding target for dinucleoside polyphosphates. J.Biol.Chem. (2019)

Release Date

2019-08-28

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Inosine-5'-monophosphate dehydrogenase