SMTL ID : 7rgq.1

HUMAN RETINAL VARIANT IMPDH1(546) TREATED WITH GTP, ATP, IMP, NAD+; INTERFACE-CENTERED

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

16 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 12 residues within 4Å: Chain A: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, D.226, L.227, N.230, K.238, K.242 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.112, A:Q.112, A:N.198, A:N.230, A:N.230, A:K.238 Salt bridges: A:K.242, A:K.242, A:K.242 GTP.5: 17 residues within 4Å: Chain A: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, H.137, F.139, S.140, G.141, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.137, A:S.140, A:D.226, A:D.226 Salt bridges: A:K.208, A:K.208, A:K.208 pi-Stacking: A:F.139, A:F.139 GTP.6: 12 residues within 4Å: Chain B: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, D.226, L.227, N.230, K.238, K.242 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.112, B:N.198, B:N.198, B:N.230, B:N.230, B:K.238 Salt bridges: B:K.238, B:K.242, B:K.242, B:K.242 GTP.10: 17 residues within 4Å: Chain B: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.112, B:V.119, B:S.140, B:T.225, B:D.226, B:D.226, B:D.226 Salt bridges: B:K.208, B:K.208 pi-Stacking: B:F.139 pi-Cation interactions: B:F.139 GTP.11: 13 residues within 4Å: Chain C: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, K.238, K.242 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.112, C:Q.112, C:N.198, C:N.230, C:N.230, C:K.238 Salt bridges: C:K.242, C:K.242, C:K.242 GTP.15: 17 residues within 4Å: Chain C: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.14 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.112, C:V.119, C:S.140, C:S.140, C:G.141, C:T.225, C:D.226, C:D.226 Salt bridges: C:K.208, C:K.208 pi-Stacking: C:F.139 pi-Cation interactions: C:F.139 GTP.16: 13 residues within 4Å: Chain D: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, K.238, K.242 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.112, D:N.198, D:N.230, D:K.238 Salt bridges: D:K.238, D:K.242, D:K.242, D:K.242 GTP.20: 17 residues within 4Å: Chain D: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.19 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Q.112, D:V.119, D:S.140, D:G.141, D:K.208, D:T.225, D:D.226, D:D.226, D:D.226 Salt bridges: D:K.208, D:K.208 pi-Stacking: D:F.139 pi-Cation interactions: D:F.139 GTP.21: 13 residues within 4Å: Chain E: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, K.238, K.242 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.111, E:Q.112, E:N.198, E:N.230, E:K.238 Salt bridges: E:K.238, E:K.242, E:K.242, E:K.242 GTP.25: 17 residues within 4Å: Chain E: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.24 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Q.112, E:V.119, E:G.141, E:K.208, E:T.225, E:D.226, E:D.226, E:D.226 Salt bridges: E:K.208, E:K.208 pi-Stacking: E:F.139 GTP.26: 12 residues within 4Å: Chain F: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, D.226, L.227, N.230, K.238, K.242 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Q.112, F:N.198, F:N.198, F:N.230, F:N.230, F:K.238 Salt bridges: F:K.238, F:K.242, F:K.242, F:K.242 GTP.30: 17 residues within 4Å: Chain F: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.29 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Q.112, F:V.119, F:S.140, F:G.141, F:T.225, F:D.226, F:D.226, F:D.226 Salt bridges: F:K.208 pi-Stacking: F:F.139 pi-Cation interactions: F:F.139 GTP.31: 13 residues within 4Å: Chain G: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, K.238, K.242 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:E.111, G:Q.112, G:Q.112, G:N.198, G:N.230, G:N.230, G:K.238 Salt bridges: G:K.242, G:K.242, G:K.242 GTP.35: 17 residues within 4Å: Chain G: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.34 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:Q.112, G:V.119, G:S.140, G:G.141, G:T.225, G:D.226, G:D.226, G:D.226 Salt bridges: G:K.208, G:K.208 pi-Stacking: G:F.139 pi-Cation interactions: G:F.139 GTP.36: 13 residues within 4Å: Chain H: E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, K.238, K.242 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:Q.112, H:Q.112, H:N.198, H:N.230, H:N.230, H:K.238 Salt bridges: H:K.238, H:K.242, H:K.242, H:K.242 GTP.40: 17 residues within 4Å: Chain H: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, F.139, S.140, G.141, K.208, I.221, A.223, T.225, D.226, K.229 Ligands: ATP.39 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:Q.112, H:V.119, H:S.140, H:T.225, H:D.226, H:D.226, H:D.226 Salt bridges: H:K.208, H:K.208 pi-Stacking: H:F.139 pi-Cation interactions: H:F.139

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 20 residues within 4Å: Chain A: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, R.322, G.326, C.331, T.333, M.414, Q.441 Chain B: I.45, A.46, H.466, Q.469 Ligands: IMP.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.93, A:T.252, A:R.253, A:S.276, A:S.276, A:T.333, B:H.466, B:Q.469, B:Q.469 Salt bridges: A:R.253 pi-Stacking: A:Y.282 pi-Cation interactions: A:R.253 NAD.7: 21 residues within 4Å: Chain B: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, M.325, G.326, T.333, M.414, Q.441 Chain C: I.45, A.46, H.466, Q.469 Ligands: IMP.8 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:H.466, C:Q.469, C:Q.469, B:H.93, B:T.252, B:R.253, B:S.276, B:S.276, B:T.333 Salt bridges: B:R.253 pi-Stacking: B:Y.282 pi-Cation interactions: B:R.253 NAD.12: 22 residues within 4Å: Chain C: P.69, H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, M.325, G.326, T.333, M.414, Q.441 Chain D: I.45, A.46, H.466, Q.469 Ligands: IMP.13 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.93, C:T.252, C:R.253, C:S.275, C:S.275, C:S.276, D:H.466, D:Q.469, D:Q.469 Salt bridges: C:R.253 pi-Stacking: C:Y.282 pi-Cation interactions: C:R.253 NAD.17: 21 residues within 4Å: Chain A: I.45, A.46, H.466, Q.469 Chain D: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, M.325, G.326, T.333, M.414, Q.441 Ligands: IMP.18 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.93, D:T.252, D:R.253, D:R.253, D:E.254, D:S.276, D:S.276, D:T.333, A:A.46, A:Q.469, A:Q.469 Salt bridges: D:R.253 pi-Stacking: D:Y.282 pi-Cation interactions: D:R.253 NAD.22: 21 residues within 4Å: Chain E: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, M.325, G.326, T.333, M.414, Q.441 Chain F: I.45, A.46, H.466, Q.469 Ligands: IMP.23 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:H.93, E:T.252, E:R.253, E:S.276, E:S.276, E:T.333, F:H.466, F:Q.469, F:Q.469 Salt bridges: E:R.253 pi-Stacking: E:Y.282 pi-Cation interactions: E:R.253 NAD.27: 20 residues within 4Å: Chain F: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, R.322, M.325, G.326, T.333, M.414, Q.441 Chain G: I.45, A.46, H.466, Q.469 Ligands: IMP.28 12 PLIP interactions: 3 interactions with chain G, 9 interactions with chain F Hydrogen bonds: G:H.466, G:Q.469, G:Q.469, F:H.93, F:T.252, F:R.253, F:S.276, F:S.276, F:T.333 Salt bridges: F:R.253 pi-Stacking: F:Y.282 pi-Cation interactions: F:R.253 NAD.32: 21 residues within 4Å: Chain G: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, R.322, M.325, G.326, T.333, M.414, Q.441 Chain H: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.33 15 PLIP interactions: 2 interactions with chain H, 13 interactions with chain G Hydrogen bonds: H:Q.469, H:Q.469, G:H.93, G:T.252, G:R.253, G:R.253, G:E.254, G:S.275, G:S.276, G:S.276, G:T.333 Salt bridges: G:R.253 pi-Stacking: G:Y.282 pi-Cation interactions: G:R.253, G:R.253 NAD.37: 21 residues within 4Å: Chain E: I.45, A.46, H.466, Q.469 Chain H: H.93, T.252, R.253, E.254, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, M.325, G.326, T.333, M.414, Q.441 Ligands: IMP.38 14 PLIP interactions: 11 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:H.93, H:T.252, H:R.253, H:R.253, H:E.254, H:S.276, H:S.276, H:T.333, E:A.46, E:Q.469, E:Q.469 Salt bridges: H:R.253 pi-Stacking: H:Y.282 pi-Cation interactions: H:R.253

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 25 residues within 4Å: Chain A: S.68, P.69, M.70, N.303, R.322, C.327, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, M.414, G.415, Q.441, G.442 Ligands: NAD.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.68, A:S.329, A:I.330, A:D.364, A:D.364, A:G.366, A:I.367, A:G.387, A:S.388, A:S.388, A:S.388, A:Y.411 IMP.8: 24 residues within 4Å: Chain B: S.68, P.69, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.68, B:S.329, B:D.364, B:D.364, B:G.366, B:I.367, B:G.387, B:S.388, B:Y.411, B:M.414, B:G.415, B:Q.441 IMP.13: 25 residues within 4Å: Chain C: S.68, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.68, C:S.329, C:D.364, C:D.364, C:G.366, C:I.367, C:G.387, C:S.388, C:S.388, C:S.388, C:Y.411, C:M.414, C:G.415, C:Q.441 IMP.18: 25 residues within 4Å: Chain D: S.68, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.17 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.68, D:S.329, D:D.364, D:D.364, D:G.366, D:I.367, D:G.387, D:S.388, D:Y.411, D:M.414, D:G.415, D:Q.441 IMP.23: 24 residues within 4Å: Chain E: S.68, P.69, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.22 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.68, E:N.303, E:S.329, E:I.330, E:D.364, E:D.364, E:G.366, E:I.367, E:G.387, E:S.388, E:Y.411, E:M.414, E:G.415, E:Q.441 IMP.28: 25 residues within 4Å: Chain F: S.68, P.69, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.27 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.68, F:S.329, F:I.330, F:D.364, F:D.364, F:G.366, F:I.367, F:G.387, F:S.388, F:Y.411, F:M.414, F:G.415, F:Q.441 IMP.33: 24 residues within 4Å: Chain G: S.68, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.32 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.68, G:S.329, G:D.364, G:D.364, G:G.366, G:I.367, G:G.387, G:S.388, G:S.388, G:Y.411, G:M.414, G:G.415, G:Q.441 IMP.38: 23 residues within 4Å: Chain H: S.68, M.70, N.303, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.37 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:S.68, H:S.329, H:I.330, H:D.364, H:D.364, H:G.366, H:I.367, H:S.388, H:Y.411, H:M.414, H:G.415, H:Q.441

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

ATP.4: 19 residues within 4Å: Chain A: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain H: R.161, K.205, K.228 Ligands: GTP.5 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:T.159, A:D.162, A:D.162, A:V.186, A:V.186, A:G.207, A:K.208, H:R.161 Salt bridges: A:R.161, A:R.161, A:R.161, A:K.208, A:K.208, A:K.208, H:R.161, H:K.228 ATP.9: 19 residues within 4Å: Chain B: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain G: R.161, K.205, K.228 Ligands: GTP.10 14 PLIP interactions: 3 interactions with chain G, 11 interactions with chain B Salt bridges: G:R.161, G:R.161, G:K.228, B:R.161, B:R.161, B:R.161 Hydrogen bonds: B:T.159, B:T.159, B:D.162, B:D.162, B:V.186, B:V.186, B:G.207, B:K.208 ATP.14: 17 residues within 4Å: Chain C: I.157, V.158, T.159, S.160, R.161, D.162, T.180, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain F: R.161, K.205 Ligands: GTP.15 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:T.159, C:T.159, C:D.162, C:D.162, C:G.207, C:K.208, C:K.208 Salt bridges: C:R.161, C:R.161, C:R.161, C:K.208, F:R.161, F:R.161, F:K.228 ATP.19: 18 residues within 4Å: Chain D: I.157, T.159, S.160, R.161, D.162, T.180, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain E: R.161, K.205, K.206, K.228 Ligands: GTP.20 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:T.159, D:S.160, D:D.162, D:V.186, D:V.186 Salt bridges: D:R.161, D:R.161, E:R.161, E:K.228 ATP.24: 18 residues within 4Å: Chain D: R.161, K.205, K.206, K.228 Chain E: I.157, T.159, S.160, R.161, D.162, T.180, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: GTP.25 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain E Salt bridges: D:R.161, D:K.228, E:R.161, E:R.161 Hydrogen bonds: E:T.159, E:D.162, E:V.186, E:V.186, E:G.207 ATP.29: 18 residues within 4Å: Chain C: R.161, K.205, K.228 Chain F: I.157, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: GTP.30 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:T.159, F:S.160, F:D.162, F:D.162, F:V.186, F:V.186, F:G.207, F:K.208, C:R.161 Salt bridges: F:R.161, F:R.161, C:R.161, C:K.228 ATP.34: 18 residues within 4Å: Chain B: R.161, K.205, K.228 Chain G: I.157, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: GTP.35 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain B Hydrogen bonds: G:T.159, G:D.162, G:D.162, G:V.186, G:G.207, G:K.208, G:K.208, B:R.161 Salt bridges: G:R.161, G:R.161, B:R.161, B:K.228 ATP.39: 19 residues within 4Å: Chain A: R.161, K.205, K.228 Chain H: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: GTP.40 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:T.159, H:D.162, H:D.162, H:V.186, H:G.207, H:K.208, H:K.208, A:R.161 Salt bridges: H:R.161, H:R.161, H:R.161, A:R.161, A:K.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burrell, A.L. et al., IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-01-12

Peptides

Inosine-5'-monophosphate dehydrogenase 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Inosine-5'-monophosphate dehydrogenase 1

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