SMTL ID : 5tc3.1

Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP and GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-octamer

Ligands

8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 26 residues within 4Å: Chain A: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, I.336, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, Q.449, G.450 Chain G: H.512 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.75, A:N.307, A:R.326, A:R.326, A:G.330, A:S.333, A:T.337, A:T.337, A:D.368, A:G.370, A:Q.372, A:G.391, A:G.392, A:Y.415, A:G.419, A:Q.449 5GP.6: 25 residues within 4Å: Chain B: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, S.420, Q.449, G.450 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.75, B:N.307, B:R.326, B:R.326, B:S.333, B:S.333, B:T.337, B:T.337, B:D.368, B:D.368, B:G.370, B:Q.372, B:G.391, B:G.392, B:Y.415, B:Q.449 Water bridges: B:G.369 5GP.10: 26 residues within 4Å: Chain C: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, I.336, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, Q.449, G.450 Chain E: H.512 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.75, C:N.307, C:R.326, C:R.326, C:G.330, C:S.333, C:T.337, C:T.337, C:D.368, C:G.370, C:Q.372, C:G.391, C:G.392, C:Y.415, C:G.419, C:Q.449 5GP.15: 25 residues within 4Å: Chain D: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, S.420, Q.449, G.450 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.75, D:N.307, D:R.326, D:R.326, D:S.333, D:S.333, D:T.337, D:T.337, D:D.368, D:D.368, D:G.370, D:Q.372, D:G.391, D:G.392, D:Y.415, D:Q.449 Water bridges: D:G.369 5GP.19: 26 residues within 4Å: Chain A: H.512 Chain E: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, I.336, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, Q.449, G.450 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.75, E:N.307, E:R.326, E:R.326, E:G.330, E:S.333, E:T.337, E:T.337, E:D.368, E:G.370, E:Q.372, E:G.391, E:G.392, E:Y.415, E:G.419, E:Q.449 5GP.24: 25 residues within 4Å: Chain F: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, S.420, Q.449, G.450 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:S.75, F:N.307, F:R.326, F:R.326, F:S.333, F:S.333, F:T.337, F:T.337, F:D.368, F:D.368, F:G.370, F:Q.372, F:G.391, F:G.392, F:Y.415, F:Q.449 Water bridges: F:G.369 5GP.28: 26 residues within 4Å: Chain C: H.512 Chain G: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, I.336, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, Q.449, G.450 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:S.75, G:N.307, G:R.326, G:R.326, G:G.330, G:S.333, G:T.337, G:T.337, G:D.368, G:G.370, G:Q.372, G:G.391, G:G.392, G:Y.415, G:G.419, G:Q.449 5GP.33: 25 residues within 4Å: Chain H: S.75, P.76, M.77, N.307, R.326, M.329, G.330, G.332, S.333, C.335, T.337, D.368, G.369, G.370, V.371, Q.372, M.389, M.390, G.391, G.392, Y.415, G.419, S.420, Q.449, G.450 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:S.75, H:N.307, H:R.326, H:R.326, H:S.333, H:S.333, H:T.337, H:T.337, H:D.368, H:D.368, H:G.370, H:Q.372, H:G.391, H:G.392, H:Y.415, H:Q.449 Water bridges: H:G.369

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 19 residues within 4Å: Chain A: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Chain B: R.168, K.208 Ligands: GDP.3, ATP.7 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.166, A:S.167, A:R.168, A:D.169, A:T.185, A:T.185, A:I.189, A:I.189, A:K.209, A:G.210, A:K.211 Water bridges: A:S.167, A:S.167 Salt bridges: A:R.168, A:K.211, A:K.211, B:R.168, B:R.168, B:R.168 ATP.7: 19 residues within 4Å: Chain A: R.168, K.208 Chain B: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Ligands: ATP.2, GDP.8 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.167, B:R.168, B:D.169, B:T.185, B:T.185, B:I.189, B:I.189, B:K.209, B:G.210, B:K.211 Water bridges: B:S.167, B:R.168, B:K.211, A:R.168, A:R.168 Salt bridges: B:R.168, B:K.211, B:K.211, A:R.168, A:R.168 ATP.11: 19 residues within 4Å: Chain C: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Chain D: R.168, K.208 Ligands: GDP.12, ATP.16 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.166, C:S.167, C:R.168, C:D.169, C:T.185, C:T.185, C:I.189, C:I.189, C:K.209, C:G.210, C:K.211 Water bridges: C:S.167, C:S.167 Salt bridges: C:R.168, C:K.211, C:K.211, D:R.168, D:R.168, D:R.168 ATP.16: 19 residues within 4Å: Chain C: R.168, K.208 Chain D: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Ligands: ATP.11, GDP.17 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.167, D:R.168, D:D.169, D:T.185, D:T.185, D:I.189, D:I.189, D:K.209, D:G.210, D:K.211 Water bridges: D:S.167, D:R.168, D:K.211, C:R.168, C:R.168 Salt bridges: D:R.168, D:K.211, D:K.211, C:R.168, C:R.168 ATP.20: 19 residues within 4Å: Chain E: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Chain F: R.168, K.208 Ligands: GDP.21, ATP.25 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.166, E:S.167, E:R.168, E:D.169, E:T.185, E:T.185, E:I.189, E:I.189, E:K.209, E:G.210, E:K.211 Water bridges: E:S.167, E:S.167 Salt bridges: E:R.168, E:K.211, E:K.211, F:R.168, F:R.168, F:R.168 ATP.25: 19 residues within 4Å: Chain E: R.168, K.208 Chain F: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Ligands: ATP.20, GDP.26 20 PLIP interactions: 16 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:S.167, F:R.168, F:D.169, F:T.185, F:T.185, F:I.189, F:I.189, F:K.209, F:G.210, F:K.211 Water bridges: F:S.167, F:R.168, F:K.211, E:R.168, E:R.168 Salt bridges: F:R.168, F:K.211, F:K.211, E:R.168, E:R.168 ATP.29: 19 residues within 4Å: Chain G: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Chain H: R.168, K.208 Ligands: GDP.30, ATP.34 19 PLIP interactions: 16 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:T.166, G:S.167, G:R.168, G:D.169, G:T.185, G:T.185, G:I.189, G:I.189, G:K.209, G:G.210, G:K.211 Water bridges: G:S.167, G:S.167 Salt bridges: G:R.168, G:K.211, G:K.211, H:R.168, H:R.168, H:R.168 ATP.34: 19 residues within 4Å: Chain G: R.168, K.208 Chain H: I.164, I.165, T.166, S.167, R.168, D.169, T.185, D.187, V.188, I.189, K.209, G.210, K.211, L.212, P.213 Ligands: ATP.29, GDP.35 20 PLIP interactions: 4 interactions with chain G, 16 interactions with chain H Water bridges: G:R.168, G:R.168, H:S.167, H:R.168, H:K.211 Salt bridges: G:R.168, G:R.168, H:R.168, H:K.211, H:K.211 Hydrogen bonds: H:S.167, H:R.168, H:D.169, H:T.185, H:T.185, H:I.189, H:I.189, H:K.209, H:G.210, H:K.211

16 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 18 residues within 4Å: Chain A: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, S.167, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.117, A:N.119, A:N.119, A:V.126, A:A.147, A:G.148, A:G.148, A:G.148, A:S.226, A:T.228, A:D.229, A:K.232 Water bridges: A:S.167, A:S.167 Salt bridges: A:K.211, A:K.211 pi-Stacking: A:F.146 pi-Cation interactions: A:F.146 GDP.4: 12 residues within 4Å: Chain A: E.118, N.119, G.120, L.197, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.118, A:N.119, A:N.201, A:N.201, A:N.233, A:K.241 Salt bridges: A:K.241, A:K.246 GDP.8: 18 residues within 4Å: Chain B: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, F.149, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Y.117, B:N.119, B:N.119, B:V.126, B:A.147, B:G.148, B:G.148, B:G.148, B:S.226, B:T.228, B:D.229, B:K.232 Water bridges: B:S.167, B:K.211, B:K.211 Salt bridges: B:K.211, B:K.211 pi-Stacking: B:F.146 pi-Cation interactions: B:F.146 GDP.9: 13 residues within 4Å: Chain B: E.118, N.119, G.120, L.197, E.198, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.119, B:N.201, B:N.201, B:N.233, B:K.241 Salt bridges: B:K.241, B:K.246 GDP.12: 18 residues within 4Å: Chain C: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, S.167, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.11 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:Y.117, C:N.119, C:N.119, C:V.126, C:A.147, C:G.148, C:G.148, C:G.148, C:S.226, C:T.228, C:D.229, C:K.232 Water bridges: C:S.167, C:S.167 Salt bridges: C:K.211, C:K.211 pi-Stacking: C:F.146 pi-Cation interactions: C:F.146 GDP.13: 12 residues within 4Å: Chain C: E.118, N.119, G.120, L.197, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.118, C:N.119, C:N.201, C:N.201, C:N.233, C:K.241 Salt bridges: C:K.241, C:K.246 GDP.17: 18 residues within 4Å: Chain D: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, F.149, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.16 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Y.117, D:N.119, D:N.119, D:V.126, D:A.147, D:G.148, D:G.148, D:G.148, D:S.226, D:T.228, D:D.229, D:K.232 Water bridges: D:S.167, D:K.211, D:K.211 Salt bridges: D:K.211, D:K.211 pi-Stacking: D:F.146 pi-Cation interactions: D:F.146 GDP.18: 13 residues within 4Å: Chain D: E.118, N.119, G.120, L.197, E.198, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.119, D:N.201, D:N.201, D:N.233, D:K.241 Salt bridges: D:K.241, D:K.246 GDP.21: 18 residues within 4Å: Chain E: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, S.167, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.20 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:Y.117, E:N.119, E:N.119, E:V.126, E:A.147, E:G.148, E:G.148, E:G.148, E:S.226, E:T.228, E:D.229, E:K.232 Water bridges: E:S.167, E:S.167 Salt bridges: E:K.211, E:K.211 pi-Stacking: E:F.146 pi-Cation interactions: E:F.146 GDP.22: 12 residues within 4Å: Chain E: E.118, N.119, G.120, L.197, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.118, E:N.119, E:N.201, E:N.201, E:N.233, E:K.241 Salt bridges: E:K.241, E:K.246 GDP.26: 18 residues within 4Å: Chain F: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, F.149, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.25 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:Y.117, F:N.119, F:N.119, F:V.126, F:A.147, F:G.148, F:G.148, F:G.148, F:S.226, F:T.228, F:D.229, F:K.232 Water bridges: F:S.167, F:K.211, F:K.211 Salt bridges: F:K.211, F:K.211 pi-Stacking: F:F.146 pi-Cation interactions: F:F.146 GDP.27: 13 residues within 4Å: Chain F: E.118, N.119, G.120, L.197, E.198, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.119, F:N.201, F:N.201, F:N.233, F:K.241 Salt bridges: F:K.241, F:K.246 GDP.30: 18 residues within 4Å: Chain G: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, S.167, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.29 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:Y.117, G:N.119, G:N.119, G:V.126, G:A.147, G:G.148, G:G.148, G:G.148, G:S.226, G:T.228, G:D.229, G:K.232 Water bridges: G:S.167, G:S.167 Salt bridges: G:K.211, G:K.211 pi-Stacking: G:F.146 pi-Cation interactions: G:F.146 GDP.31: 12 residues within 4Å: Chain G: E.118, N.119, G.120, L.197, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.118, G:N.119, G:N.201, G:N.201, G:N.233, G:K.241 Salt bridges: G:K.241, G:K.246 GDP.35: 18 residues within 4Å: Chain H: K.116, Y.117, E.118, N.119, I.122, P.125, V.126, F.146, A.147, G.148, F.149, K.211, M.224, S.226, T.228, D.229, K.232 Ligands: ATP.34 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:Y.117, H:N.119, H:N.119, H:V.126, H:A.147, H:G.148, H:G.148, H:G.148, H:S.226, H:T.228, H:D.229, H:K.232 Water bridges: H:S.167, H:K.211, H:K.211 Salt bridges: H:K.211, H:K.211 pi-Stacking: H:F.146 pi-Cation interactions: H:F.146 GDP.36: 13 residues within 4Å: Chain H: E.118, N.119, G.120, L.197, E.198, N.201, L.225, S.226, D.229, L.230, N.233, K.241, K.246 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:N.119, H:N.201, H:N.201, H:N.233, H:K.241 Salt bridges: H:K.241, H:K.246

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

ACT.5: 2 residues within 4Å: Chain A: R.261, W.293 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.293 ACT.14: 2 residues within 4Å: Chain C: R.261, W.293 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.293 ACT.23: 2 residues within 4Å: Chain E: R.261, W.293 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.293 ACT.32: 2 residues within 4Å: Chain G: R.261, W.293 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:W.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buey, R.M. et al., A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases. Sci Rep (2017)

Release Date

2017-06-14

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Inosine-5'-monophosphate dehydrogenase

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