SMTL ID : 4z87.3 (2 other biounits)

Structure of the IMP dehydrogenase from Ashbya gossypii bound to GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

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

5GP.1: 28 residues within 4Å: Chain A: S.77, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 Chain D: H.514 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.77, A:N.309, A:R.328, A:S.335, A:S.335, A:T.339, A:T.339, A:D.370, A:D.370, A:G.372, A:Q.374, A:G.393, A:G.394, A:Y.417, A:M.420, A:G.421, A:S.422, A:Q.451 Water bridges: A:G.332, A:G.334, A:G.371, A:G.371, A:M.395 5GP.6: 28 residues within 4Å: Chain A: H.514 Chain B: S.77, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:S.77, B:N.309, B:R.328, B:S.335, B:S.335, B:T.339, B:T.339, B:D.370, B:D.370, B:G.372, B:Q.374, B:G.393, B:G.394, B:Y.417, B:M.420, B:G.421, B:S.422, B:Q.451 Water bridges: B:G.332, B:G.334, B:G.371, B:G.371, B:M.395 5GP.11: 28 residues within 4Å: Chain B: H.514 Chain C: S.77, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:S.77, C:N.309, C:R.328, C:S.335, C:S.335, C:T.339, C:T.339, C:D.370, C:D.370, C:G.372, C:Q.374, C:G.393, C:G.394, C:Y.417, C:M.420, C:G.421, C:S.422, C:Q.451 Water bridges: C:G.332, C:G.334, C:G.371, C:G.371, C:M.395 5GP.16: 28 residues within 4Å: Chain C: H.514 Chain D: S.77, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:S.77, D:N.309, D:R.328, D:S.335, D:S.335, D:T.339, D:T.339, D:D.370, D:D.370, D:G.372, D:Q.374, D:G.393, D:G.394, D:Y.417, D:M.420, D:G.421, D:S.422, D:Q.451 Water bridges: D:G.332, D:G.334, D:G.371, D:G.371, D:M.395 5GP.21: 30 residues within 4Å: Chain E: S.77, P.78, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 Chain F: H.514 Ligands: ACT.26 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:S.77, E:N.309, E:R.328, E:S.335, E:S.335, E:T.339, E:T.339, E:D.370, E:D.370, E:G.372, E:G.393, E:G.394, E:M.420, E:G.421, E:S.422, E:Q.451 Water bridges: E:G.332, E:G.334, E:G.371, E:V.373 5GP.28: 30 residues within 4Å: Chain F: S.77, P.78, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 Chain H: H.514 Ligands: ACT.33 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:S.77, F:N.309, F:R.328, F:S.335, F:S.335, F:T.339, F:T.339, F:D.370, F:D.370, F:G.372, F:G.393, F:G.394, F:M.420, F:G.421, F:S.422, F:Q.451 Water bridges: F:G.332, F:G.334, F:G.371, F:V.373 5GP.35: 30 residues within 4Å: Chain E: H.514 Chain G: S.77, P.78, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 Ligands: ACT.40 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:S.77, G:N.309, G:R.328, G:S.335, G:S.335, G:T.339, G:T.339, G:D.370, G:D.370, G:G.372, G:G.393, G:G.394, G:M.420, G:G.421, G:S.422, G:Q.451 Water bridges: G:G.332, G:G.334, G:G.371, G:V.373 5GP.42: 30 residues within 4Å: Chain G: H.514 Chain H: S.77, P.78, M.79, S.282, N.309, R.328, G.332, G.334, S.335, I.336, C.337, T.339, D.370, G.371, G.372, V.373, Q.374, M.391, M.392, G.393, G.394, Y.417, G.419, M.420, G.421, S.422, Q.451, G.452 Ligands: ACT.47 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:S.77, H:N.309, H:R.328, H:S.335, H:S.335, H:T.339, H:T.339, H:D.370, H:D.370, H:G.372, H:G.393, H:G.394, H:M.420, H:G.421, H:S.422, H:Q.451 Water bridges: H:G.332, H:G.334, H:G.371, H:V.373

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

GDP.2: 15 residues within 4Å: Chain A: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 Chain F: R.170, K.210 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:T.168, A:S.169, A:S.169, A:S.169, A:R.170, A:D.171, A:T.187, A:T.187, A:I.191, A:K.211, A:G.212, F:K.210 Salt bridges: A:D.189, F:R.170, F:R.170 GDP.3: 16 residues within 4Å: Chain A: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.118, A:Y.119, A:N.121, A:N.121, A:V.128, A:A.149, A:G.150, A:G.150, A:S.228, A:T.230, A:D.231, A:K.234 Water bridges: A:A.149, A:S.169 Salt bridges: A:K.213, A:K.213 pi-Stacking: A:F.148 pi-Cation interactions: A:F.148 GDP.4: 13 residues within 4Å: Chain A: E.120, N.121, G.122, L.199, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.121, A:N.203, A:N.203, A:N.203, A:K.243, A:K.248 Water bridges: A:D.231, A:N.235, A:P.239 Salt bridges: A:K.243, A:K.248 GDP.7: 15 residues within 4Å: Chain B: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 Chain H: R.170, K.210 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain H Hydrogen bonds: B:T.168, B:S.169, B:S.169, B:S.169, B:R.170, B:D.171, B:T.187, B:T.187, B:I.191, B:K.211, B:G.212, H:K.210 Salt bridges: B:D.189, H:R.170, H:R.170 GDP.8: 16 residues within 4Å: Chain B: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.118, B:Y.119, B:N.121, B:N.121, B:V.128, B:A.149, B:G.150, B:G.150, B:S.228, B:T.230, B:D.231, B:K.234 Water bridges: B:A.149, B:S.169 Salt bridges: B:K.213, B:K.213 pi-Stacking: B:F.148 pi-Cation interactions: B:F.148 GDP.9: 13 residues within 4Å: Chain B: E.120, N.121, G.122, L.199, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.121, B:N.203, B:N.203, B:N.203, B:K.243, B:K.248 Water bridges: B:D.231, B:N.235, B:P.239 Salt bridges: B:K.243, B:K.248 GDP.12: 15 residues within 4Å: Chain C: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 Chain G: R.170, K.210 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain G Hydrogen bonds: C:T.168, C:S.169, C:S.169, C:S.169, C:R.170, C:D.171, C:T.187, C:T.187, C:I.191, C:K.211, C:G.212, G:K.210 Salt bridges: C:D.189, G:R.170, G:R.170 GDP.13: 16 residues within 4Å: Chain C: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.118, C:Y.119, C:N.121, C:N.121, C:V.128, C:A.149, C:G.150, C:G.150, C:S.228, C:T.230, C:D.231, C:K.234 Water bridges: C:A.149, C:S.169 Salt bridges: C:K.213, C:K.213 pi-Stacking: C:F.148 pi-Cation interactions: C:F.148 GDP.14: 13 residues within 4Å: Chain C: E.120, N.121, G.122, L.199, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.121, C:N.203, C:N.203, C:N.203, C:K.243, C:K.248 Water bridges: C:D.231, C:N.235, C:P.239 Salt bridges: C:K.243, C:K.248 GDP.17: 15 residues within 4Å: Chain D: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 Chain E: R.170, K.210 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:T.168, D:S.169, D:S.169, D:S.169, D:R.170, D:D.171, D:T.187, D:T.187, D:I.191, D:K.211, D:G.212, E:K.210 Salt bridges: D:D.189, E:R.170, E:R.170 GDP.18: 16 residues within 4Å: Chain D: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:K.118, D:Y.119, D:N.121, D:N.121, D:V.128, D:A.149, D:G.150, D:G.150, D:S.228, D:T.230, D:D.231, D:K.234 Water bridges: D:A.149, D:S.169 Salt bridges: D:K.213, D:K.213 pi-Stacking: D:F.148 pi-Cation interactions: D:F.148 GDP.19: 13 residues within 4Å: Chain D: E.120, N.121, G.122, L.199, N.203, K.207, L.227, S.228, D.231, L.232, N.235, K.243, K.248 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.121, D:N.203, D:N.203, D:N.203, D:K.243, D:K.248 Water bridges: D:D.231, D:N.235, D:P.239 Salt bridges: D:K.243, D:K.248 GDP.22: 15 residues within 4Å: Chain D: R.170, K.210 Chain E: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.169, E:R.170, E:D.171, E:T.187, E:I.191, E:K.211, E:G.212 pi-Cation interactions: E:K.211 Salt bridges: D:R.170, D:R.170 GDP.23: 16 residues within 4Å: Chain E: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.119, E:N.121, E:N.121, E:V.128, E:A.149, E:G.150, E:G.150, E:S.228, E:T.230, E:D.231, E:K.234 Water bridges: E:G.150 Salt bridges: E:K.213, E:K.213 pi-Stacking: E:F.148 pi-Cation interactions: E:F.148 GDP.24: 13 residues within 4Å: Chain E: E.120, N.121, G.122, N.198, L.199, E.200, N.203, L.227, D.231, L.232, N.235, K.243, K.248 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:E.120, E:N.121, E:L.199, E:N.203, E:N.203, E:N.235, E:K.243, E:K.248 Salt bridges: E:K.248, E:K.248 GDP.29: 15 residues within 4Å: Chain A: R.170, K.210 Chain F: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:S.169, F:R.170, F:D.171, F:T.187, F:I.191, F:K.211, F:G.212 pi-Cation interactions: F:K.211 Salt bridges: A:R.170, A:R.170 GDP.30: 16 residues within 4Å: Chain F: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Y.119, F:N.121, F:N.121, F:V.128, F:A.149, F:G.150, F:G.150, F:S.228, F:T.230, F:D.231, F:K.234 Water bridges: F:G.150 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.148 pi-Cation interactions: F:F.148 GDP.31: 13 residues within 4Å: Chain F: E.120, N.121, G.122, N.198, L.199, E.200, N.203, L.227, D.231, L.232, N.235, K.243, K.248 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:E.120, F:N.121, F:L.199, F:N.203, F:N.203, F:N.235, F:K.243, F:K.248 Salt bridges: F:K.248, F:K.248 GDP.36: 15 residues within 4Å: Chain C: R.170, K.210 Chain G: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:S.169, G:R.170, G:D.171, G:T.187, G:I.191, G:K.211, G:G.212 pi-Cation interactions: G:K.211 Salt bridges: C:R.170, C:R.170 GDP.37: 16 residues within 4Å: Chain G: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:Y.119, G:N.121, G:N.121, G:V.128, G:A.149, G:G.150, G:G.150, G:S.228, G:T.230, G:D.231, G:K.234 Water bridges: G:G.150 Salt bridges: G:K.213, G:K.213 pi-Stacking: G:F.148 pi-Cation interactions: G:F.148 GDP.38: 13 residues within 4Å: Chain G: E.120, N.121, G.122, N.198, L.199, E.200, N.203, L.227, D.231, L.232, N.235, K.243, K.248 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:E.120, G:N.121, G:L.199, G:N.203, G:N.203, G:N.235, G:K.243, G:K.248 Salt bridges: G:K.248, G:K.248 GDP.43: 15 residues within 4Å: Chain B: R.170, K.210 Chain H: I.166, I.167, T.168, S.169, R.170, D.171, T.187, D.189, V.190, I.191, K.211, G.212, K.213 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:S.169, H:R.170, H:D.171, H:T.187, H:I.191, H:K.211, H:G.212 pi-Cation interactions: H:K.211 Salt bridges: B:R.170, B:R.170 GDP.44: 16 residues within 4Å: Chain H: K.118, Y.119, E.120, N.121, I.124, P.127, V.128, F.148, A.149, G.150, K.213, M.226, S.228, T.230, D.231, K.234 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:Y.119, H:N.121, H:N.121, H:V.128, H:A.149, H:G.150, H:G.150, H:S.228, H:T.230, H:D.231, H:K.234 Water bridges: H:G.150 Salt bridges: H:K.213, H:K.213 pi-Stacking: H:F.148 pi-Cation interactions: H:F.148 GDP.45: 13 residues within 4Å: Chain H: E.120, N.121, G.122, N.198, L.199, E.200, N.203, L.227, D.231, L.232, N.235, K.243, K.248 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:E.120, H:N.121, H:L.199, H:N.203, H:N.203, H:N.235, H:K.243, H:K.248 Salt bridges: H:K.248, H:K.248

8 x K: POTASSIUM ION(Non-covalent)

K.5: 7 residues within 4Å: Chain A: G.332, G.334, C.337 Chain D: E.510, G.511, G.512, H.514 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Metal complexes: A:G.332, A:G.334, A:C.337, D:G.511, D:G.512 K.10: 7 residues within 4Å: Chain A: E.510, G.511, G.512, H.514 Chain B: G.332, G.334, C.337 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.332, B:G.334, B:C.337, A:G.511, A:G.512 K.15: 7 residues within 4Å: Chain B: E.510, G.511, G.512, H.514 Chain C: G.332, G.334, C.337 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:G.511, B:G.512, C:G.332, C:G.334, C:C.337 K.20: 7 residues within 4Å: Chain C: E.510, G.511, G.512, H.514 Chain D: G.332, G.334, C.337 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:G.511, C:G.512, D:G.332, D:G.334, D:C.337 K.25: 8 residues within 4Å: Chain E: G.332, S.333, G.334, C.337 Chain F: E.510, G.511, G.512, H.514 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Metal complexes: F:E.510, F:G.511, F:G.512, E:G.334, E:C.337 K.32: 8 residues within 4Å: Chain F: G.332, S.333, G.334, C.337 Chain H: E.510, G.511, G.512, H.514 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain H Metal complexes: F:G.334, F:C.337, H:E.510, H:G.511, H:G.512 K.39: 8 residues within 4Å: Chain E: E.510, G.511, G.512, H.514 Chain G: G.332, S.333, G.334, C.337 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain G Metal complexes: E:E.510, E:G.511, E:G.512, G:G.334, G:C.337 K.46: 8 residues within 4Å: Chain G: E.510, G.511, G.512, H.514 Chain H: G.332, S.333, G.334, C.337 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Metal complexes: G:E.510, G:G.511, G:G.512, H:G.334, H:C.337

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

ACT.26: 6 residues within 4Å: Chain E: D.280, S.281, S.282, R.328, M.420 Ligands: 5GP.21 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.280, E:S.281 Water bridges: E:R.328 Salt bridges: E:R.328 ACT.27: 5 residues within 4Å: Chain E: L.94, L.240, I.467, P.468, Y.471 No protein-ligand interaction detected (PLIP) ACT.33: 6 residues within 4Å: Chain F: D.280, S.281, S.282, R.328, M.420 Ligands: 5GP.28 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.280, F:S.281 Water bridges: F:R.328 Salt bridges: F:R.328 ACT.34: 5 residues within 4Å: Chain F: L.94, L.240, I.467, P.468, Y.471 No protein-ligand interaction detected (PLIP) ACT.40: 6 residues within 4Å: Chain G: D.280, S.281, S.282, R.328, M.420 Ligands: 5GP.35 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:D.280, G:S.281 Water bridges: G:R.328 Salt bridges: G:R.328 ACT.41: 5 residues within 4Å: Chain G: L.94, L.240, I.467, P.468, Y.471 No protein-ligand interaction detected (PLIP) ACT.47: 6 residues within 4Å: Chain H: D.280, S.281, S.282, R.328, M.420 Ligands: 5GP.42 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:D.280, H:S.281 Water bridges: H:R.328 Salt bridges: H:R.328 ACT.48: 5 residues within 4Å: Chain H: L.94, L.240, I.467, P.468, Y.471 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buey, R.M. et al., Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun (2015)

Release Date

2015-11-25

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
D

D
D

E
C

F
C

G
C

H
C

Inosine-5'-monophosphate dehydrogenase

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