SMTL ID : 6i0m.1

Structure of human IMP dehydrogenase, isoform 2, bound to GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-octamer

Ligands

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

5GP.1: 22 residues within 4Å: Chain A: S.71, P.72, M.73, S.279, N.306, R.325, G.329, S.330, G.331, S.332, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, M.417, G.418 Ligands: SO4.11 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.71, A:R.325, A:R.325, A:T.336, A:G.369, A:G.390, A:S.391 Water bridges: A:R.325, A:G.329, A:G.329 5GP.12: 19 residues within 4Å: Chain B: S.71, M.73, N.306, R.325, G.329, S.330, G.331, S.332, I.335, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, L.392 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.71, B:R.325, B:R.325, B:S.332, B:S.332, B:I.335, B:I.335, B:I.335, B:T.336, B:D.367, B:D.367, B:G.369, B:G.390, B:S.391 5GP.19: 22 residues within 4Å: Chain C: S.71, P.72, M.73, S.279, N.306, R.325, G.329, S.330, G.331, S.332, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, M.417, G.418 Ligands: SO4.29 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.71, C:R.325, C:R.325, C:T.336, C:G.369, C:G.390, C:S.391 Water bridges: C:R.325, C:G.329, C:G.329 5GP.30: 19 residues within 4Å: Chain D: S.71, M.73, N.306, R.325, G.329, S.330, G.331, S.332, I.335, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, L.392 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.71, D:R.325, D:R.325, D:S.332, D:S.332, D:I.335, D:I.335, D:I.335, D:T.336, D:D.367, D:D.367, D:G.369, D:G.390, D:S.391 5GP.37: 22 residues within 4Å: Chain E: S.71, P.72, M.73, S.279, N.306, R.325, G.329, S.330, G.331, S.332, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, M.417, G.418 Ligands: SO4.47 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.71, E:R.325, E:R.325, E:T.336, E:G.369, E:G.390, E:S.391 Water bridges: E:R.325, E:G.329, E:G.329 5GP.48: 19 residues within 4Å: Chain F: S.71, M.73, N.306, R.325, G.329, S.330, G.331, S.332, I.335, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, L.392 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.71, F:R.325, F:R.325, F:S.332, F:S.332, F:I.335, F:I.335, F:I.335, F:T.336, F:D.367, F:D.367, F:G.369, F:G.390, F:S.391 5GP.55: 22 residues within 4Å: Chain G: S.71, P.72, M.73, S.279, N.306, R.325, G.329, S.330, G.331, S.332, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, M.417, G.418 Ligands: SO4.65 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.71, G:R.325, G:R.325, G:T.336, G:G.369, G:G.390, G:S.391 Water bridges: G:R.325, G:G.329, G:G.329 5GP.66: 19 residues within 4Å: Chain H: S.71, M.73, N.306, R.325, G.329, S.330, G.331, S.332, I.335, T.336, D.367, G.368, G.369, I.370, M.388, M.389, G.390, S.391, L.392 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.71, H:R.325, H:R.325, H:S.332, H:S.332, H:I.335, H:I.335, H:I.335, H:T.336, H:D.367, H:D.367, H:G.369, H:G.390, H:S.391

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

GDP.2: 17 residues within 4Å: Chain A: I.160, I.161, S.162, S.163, R.164, D.165, T.183, D.187, L.188, V.189, K.209, G.210, K.211, P.213 Chain B: R.164, K.208 Ligands: GDP.3 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.162, A:S.163, A:D.165, A:D.187, A:V.189, A:K.209, A:G.210, B:K.208 Salt bridges: A:R.164, B:R.164, B:R.164 GDP.3: 17 residues within 4Å: Chain A: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, K.211, I.224, A.226, T.228, D.229, K.232 Ligands: GDP.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.115, A:V.122, A:C.143, A:G.144, A:G.144, A:T.228, A:D.229, A:D.229, A:D.229, A:K.232 Salt bridges: A:K.211, A:K.211 pi-Stacking: A:F.142 pi-Cation interactions: A:F.142 GDP.4: 13 residues within 4Å: Chain A: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, K.241, K.245 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.114, A:Q.115, A:N.201, A:N.201, A:K.241 Water bridges: A:L.197 Salt bridges: A:D.229, A:K.245 GDP.13: 16 residues within 4Å: Chain A: R.164, K.208 Chain B: I.160, I.161, S.162, S.163, R.164, D.165, T.183, L.188, V.189, K.209, G.210, K.211, L.212, P.213 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.162, B:S.162, B:S.163, B:S.163, B:S.163, B:D.165, B:L.188, B:L.188, B:V.189, B:K.209, B:G.210, B:K.211 Salt bridges: B:R.164, A:R.164, A:R.164 GDP.14: 17 residues within 4Å: Chain B: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, S.163, K.211, I.224, A.226, T.228, D.229, K.232 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Y.113, B:Q.115, B:V.122, B:C.143, B:G.144, B:G.144, B:G.144, B:T.228, B:D.229, B:K.232 Salt bridges: B:K.211, B:K.211 pi-Stacking: B:F.142 pi-Cation interactions: B:F.142 GDP.15: 14 residues within 4Å: Chain B: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, P.237, K.241, K.245 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.115, B:N.201, B:N.201, B:N.233, B:P.237, B:K.241 Salt bridges: B:K.241, B:K.245 GDP.20: 17 residues within 4Å: Chain C: I.160, I.161, S.162, S.163, R.164, D.165, T.183, D.187, L.188, V.189, K.209, G.210, K.211, P.213 Chain D: R.164, K.208 Ligands: GDP.21 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.162, C:S.163, C:D.165, C:D.187, C:V.189, C:K.209, C:G.210, D:K.208 Salt bridges: C:R.164, D:R.164, D:R.164 GDP.21: 17 residues within 4Å: Chain C: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, K.211, I.224, A.226, T.228, D.229, K.232 Ligands: GDP.20 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.115, C:V.122, C:C.143, C:G.144, C:G.144, C:T.228, C:D.229, C:D.229, C:D.229, C:K.232 Salt bridges: C:K.211, C:K.211 pi-Stacking: C:F.142 pi-Cation interactions: C:F.142 GDP.22: 13 residues within 4Å: Chain C: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, K.241, K.245 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.114, C:Q.115, C:N.201, C:N.201, C:K.241 Water bridges: C:L.197 Salt bridges: C:D.229, C:K.245 GDP.31: 16 residues within 4Å: Chain C: R.164, K.208 Chain D: I.160, I.161, S.162, S.163, R.164, D.165, T.183, L.188, V.189, K.209, G.210, K.211, L.212, P.213 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.162, D:S.162, D:S.163, D:S.163, D:S.163, D:D.165, D:L.188, D:L.188, D:V.189, D:K.209, D:G.210, D:K.211 Salt bridges: D:R.164, C:R.164, C:R.164 GDP.32: 17 residues within 4Å: Chain D: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, S.163, K.211, I.224, A.226, T.228, D.229, K.232 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Y.113, D:Q.115, D:V.122, D:C.143, D:G.144, D:G.144, D:G.144, D:T.228, D:D.229, D:K.232 Salt bridges: D:K.211, D:K.211 pi-Stacking: D:F.142 pi-Cation interactions: D:F.142 GDP.33: 14 residues within 4Å: Chain D: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, P.237, K.241, K.245 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.115, D:N.201, D:N.201, D:N.233, D:P.237, D:K.241 Salt bridges: D:K.241, D:K.245 GDP.38: 17 residues within 4Å: Chain E: I.160, I.161, S.162, S.163, R.164, D.165, T.183, D.187, L.188, V.189, K.209, G.210, K.211, P.213 Chain F: R.164, K.208 Ligands: GDP.39 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:S.162, E:S.163, E:D.165, E:D.187, E:V.189, E:K.209, E:G.210, F:K.208 Salt bridges: E:R.164, F:R.164, F:R.164 GDP.39: 17 residues within 4Å: Chain E: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, K.211, I.224, A.226, T.228, D.229, K.232 Ligands: GDP.38 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.115, E:V.122, E:C.143, E:G.144, E:G.144, E:T.228, E:D.229, E:D.229, E:D.229, E:K.232 Salt bridges: E:K.211, E:K.211 pi-Stacking: E:F.142 pi-Cation interactions: E:F.142 GDP.40: 13 residues within 4Å: Chain E: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, K.241, K.245 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.114, E:Q.115, E:N.201, E:N.201, E:K.241 Water bridges: E:L.197 Salt bridges: E:D.229, E:K.245 GDP.49: 16 residues within 4Å: Chain E: R.164, K.208 Chain F: I.160, I.161, S.162, S.163, R.164, D.165, T.183, L.188, V.189, K.209, G.210, K.211, L.212, P.213 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.162, F:S.162, F:S.163, F:S.163, F:S.163, F:D.165, F:L.188, F:L.188, F:V.189, F:K.209, F:G.210, F:K.211 Salt bridges: F:R.164, E:R.164, E:R.164 GDP.50: 17 residues within 4Å: Chain F: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, S.163, K.211, I.224, A.226, T.228, D.229, K.232 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Y.113, F:Q.115, F:V.122, F:C.143, F:G.144, F:G.144, F:G.144, F:T.228, F:D.229, F:K.232 Salt bridges: F:K.211, F:K.211 pi-Stacking: F:F.142 pi-Cation interactions: F:F.142 GDP.51: 14 residues within 4Å: Chain F: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, P.237, K.241, K.245 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:Q.115, F:N.201, F:N.201, F:N.233, F:P.237, F:K.241 Salt bridges: F:K.241, F:K.245 GDP.56: 17 residues within 4Å: Chain G: I.160, I.161, S.162, S.163, R.164, D.165, T.183, D.187, L.188, V.189, K.209, G.210, K.211, P.213 Chain H: R.164, K.208 Ligands: GDP.57 11 PLIP interactions: 8 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:S.162, G:S.163, G:D.165, G:D.187, G:V.189, G:K.209, G:G.210, H:K.208 Salt bridges: G:R.164, H:R.164, H:R.164 GDP.57: 17 residues within 4Å: Chain G: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, K.211, I.224, A.226, T.228, D.229, K.232 Ligands: GDP.56 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:Q.115, G:V.122, G:C.143, G:G.144, G:G.144, G:T.228, G:D.229, G:D.229, G:D.229, G:K.232 Salt bridges: G:K.211, G:K.211 pi-Stacking: G:F.142 pi-Cation interactions: G:F.142 GDP.58: 13 residues within 4Å: Chain G: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, K.241, K.245 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.114, G:Q.115, G:N.201, G:N.201, G:K.241 Water bridges: G:L.197 Salt bridges: G:D.229, G:K.245 GDP.67: 16 residues within 4Å: Chain G: R.164, K.208 Chain H: I.160, I.161, S.162, S.163, R.164, D.165, T.183, L.188, V.189, K.209, G.210, K.211, L.212, P.213 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:S.162, H:S.162, H:S.163, H:S.163, H:S.163, H:D.165, H:L.188, H:L.188, H:V.189, H:K.209, H:G.210, H:K.211 Salt bridges: H:R.164, G:R.164, G:R.164 GDP.68: 17 residues within 4Å: Chain H: K.112, Y.113, E.114, Q.115, I.118, P.121, V.122, F.142, C.143, G.144, S.163, K.211, I.224, A.226, T.228, D.229, K.232 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Y.113, H:Q.115, H:V.122, H:C.143, H:G.144, H:G.144, H:G.144, H:T.228, H:D.229, H:K.232 Salt bridges: H:K.211, H:K.211 pi-Stacking: H:F.142 pi-Cation interactions: H:F.142 GDP.69: 14 residues within 4Å: Chain H: E.114, Q.115, G.116, L.197, K.198, N.201, I.225, A.226, D.229, L.230, N.233, P.237, K.241, K.245 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:Q.115, H:N.201, H:N.201, H:N.233, H:P.237, H:K.241 Salt bridges: H:K.241, H:K.245

40 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: F.117, A.193, G.194, I.195, I.214, A.223 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: P.192, I.195, I.203 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: G.331, G.369, Q.371 Chain G: V.502, E.503, G.505 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: V.52, D.53, L.54, K.65, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: H.256, E.257, D.258 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain A: A.395, T.396, T.397, A.399, P.400, G.401, Y.403 Chain B: L.516 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain A: N.306, G.327, M.328, G.329, S.330, D.367, G.368 Ligands: 5GP.1 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: F.117, A.193, G.194, I.195, I.214, V.222 Ligand excluded by PLIP SO4.17: 9 residues within 4Å: Chain B: V.52, D.53, L.54, T.55, K.65, T.66, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: Q.481, A.484 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: F.117, A.193, G.194, I.195, I.214, A.223 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: P.192, I.195, I.203 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain C: G.331, G.369, Q.371 Chain E: V.502, E.503, G.505 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain C: V.52, D.53, L.54, K.65, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: H.256, E.257, D.258 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain C: A.395, T.396, T.397, A.399, P.400, G.401, Y.403 Chain D: L.516 Ligand excluded by PLIP SO4.29: 8 residues within 4Å: Chain C: N.306, G.327, M.328, G.329, S.330, D.367, G.368 Ligands: 5GP.19 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain D: F.117, A.193, G.194, I.195, I.214, V.222 Ligand excluded by PLIP SO4.35: 9 residues within 4Å: Chain D: V.52, D.53, L.54, T.55, K.65, T.66, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain D: Q.481, A.484 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain E: F.117, A.193, G.194, I.195, I.214, A.223 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain E: P.192, I.195, I.203 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain A: V.502, E.503, G.505 Chain E: G.331, G.369, Q.371 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain E: V.52, D.53, L.54, K.65, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain E: H.256, E.257, D.258 Ligand excluded by PLIP SO4.46: 8 residues within 4Å: Chain E: A.395, T.396, T.397, A.399, P.400, G.401, Y.403 Chain F: L.516 Ligand excluded by PLIP SO4.47: 8 residues within 4Å: Chain E: N.306, G.327, M.328, G.329, S.330, D.367, G.368 Ligands: 5GP.37 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain F: F.117, A.193, G.194, I.195, I.214, V.222 Ligand excluded by PLIP SO4.53: 9 residues within 4Å: Chain F: V.52, D.53, L.54, T.55, K.65, T.66, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain F: Q.481, A.484 Ligand excluded by PLIP SO4.59: 6 residues within 4Å: Chain G: F.117, A.193, G.194, I.195, I.214, A.223 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain G: P.192, I.195, I.203 Ligand excluded by PLIP SO4.61: 6 residues within 4Å: Chain C: V.502, E.503, G.505 Chain G: G.331, G.369, Q.371 Ligand excluded by PLIP SO4.62: 7 residues within 4Å: Chain G: V.52, D.53, L.54, K.65, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain G: H.256, E.257, D.258 Ligand excluded by PLIP SO4.64: 8 residues within 4Å: Chain G: A.395, T.396, T.397, A.399, P.400, G.401, Y.403 Chain H: L.516 Ligand excluded by PLIP SO4.65: 8 residues within 4Å: Chain G: N.306, G.327, M.328, G.329, S.330, D.367, G.368 Ligands: 5GP.55 Ligand excluded by PLIP SO4.70: 6 residues within 4Å: Chain H: F.117, A.193, G.194, I.195, I.214, V.222 Ligand excluded by PLIP SO4.71: 9 residues within 4Å: Chain H: V.52, D.53, L.54, T.55, K.65, T.66, L.238, I.464, Q.468 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain H: Q.481, A.484 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Justel, D. et al., A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity. J. Mol. Biol. (2019)

Release Date

2019-01-30

Peptides

Inosine-5'-monophosphate dehydrogenase 2: 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 2

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