SMTL ID : 7res.1

HUMAN IMPDH1 TREATED WITH ATP, IMP, AND NAD+, OCTAMER-CENTERED

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: I.157, T.159, S.160, R.161, D.162, T.180, E.184, V.186, K.206, G.207, K.208 Chain H: R.161, K.205 Ligands: ATP.2, ATP.29 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:T.159, A:S.160, A:R.161, A:R.161, A:D.162, A:K.206, A:G.207, A:K.208, A:K.208, H:K.205 Salt bridges: A:R.161, H:R.161, H:R.161 ATP.2: 14 residues within 4Å: Chain A: I.115, P.118, V.119, K.134, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.119, A:S.140, A:G.141, A:G.141, A:S.160, A:T.225, A:D.226 Salt bridges: A:K.134, A:K.208, A:K.208 pi-Stacking: A:F.139, A:F.139 ATP.5: 14 residues within 4Å: Chain B: I.157, T.159, S.160, R.161, D.162, T.180, E.184, V.186, K.206, G.207, K.208 Chain G: R.161 Ligands: ATP.6, ATP.25 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain B Salt bridges: G:R.161, G:R.161, B:R.161 Hydrogen bonds: B:T.159, B:S.160, B:R.161, B:R.161, B:D.162, B:G.207, B:K.208, B:K.208 ATP.6: 15 residues within 4Å: Chain B: I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:V.119, B:S.140, B:G.141, B:S.160, B:S.160, B:T.225, B:D.226 Salt bridges: B:K.134, B:K.208, B:K.208 pi-Stacking: B:F.139, B:F.139 ATP.9: 14 residues within 4Å: Chain C: I.157, T.159, S.160, R.161, D.162, T.180, E.184, K.206, G.207, K.208 Chain F: R.161, K.205 Ligands: ATP.10, ATP.21 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:S.160, C:R.161, C:R.161, C:D.162, C:G.207, C:K.208, C:K.208, F:K.205 Salt bridges: C:R.161, F:R.161, F:R.161, F:R.161 ATP.10: 14 residues within 4Å: Chain C: I.115, P.118, V.119, K.134, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.119, C:S.140, C:G.141, C:G.141, C:S.160, C:K.208, C:T.225, C:T.225, C:D.226 Salt bridges: C:K.134, C:K.208, C:K.208 pi-Stacking: C:F.139, C:F.139 ATP.13: 14 residues within 4Å: Chain D: I.157, T.159, S.160, R.161, D.162, T.180, E.184, K.206, G.207, K.208 Chain E: R.161, K.205 Ligands: ATP.14, ATP.17 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.159, D:R.161, D:R.161, D:D.162, D:K.206, D:G.207, D:K.208, D:K.208, E:K.205 Salt bridges: D:R.161, D:K.206, E:R.161, E:R.161, E:R.161 pi-Cation interactions: D:K.206 ATP.14: 14 residues within 4Å: Chain D: I.115, P.118, V.119, K.134, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.13 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.119, D:S.140, D:G.141, D:S.160, D:S.160, D:T.225, D:D.226 Salt bridges: D:K.134, D:K.208, D:K.208 pi-Stacking: D:F.139, D:F.139 ATP.17: 15 residues within 4Å: Chain D: R.161, K.205 Chain E: I.157, T.159, S.160, R.161, D.162, T.180, E.184, V.186, K.206, G.207, K.208 Ligands: ATP.13, ATP.18 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:T.159, E:S.160, E:R.161, E:D.162, E:T.180, E:K.206, E:G.207, E:K.208, E:K.208, D:K.205, D:K.205 Salt bridges: E:R.161, D:R.161, D:R.161 ATP.18: 15 residues within 4Å: Chain E: I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.17 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.119, E:S.140, E:G.141, E:G.141, E:S.160, E:T.225, E:D.226 Salt bridges: E:K.134, E:K.208, E:K.208 pi-Stacking: E:F.139, E:F.139 ATP.21: 14 residues within 4Å: Chain C: R.161, K.205 Chain F: I.157, T.159, S.160, R.161, D.162, T.180, E.184, K.206, G.207, K.208 Ligands: ATP.9, ATP.22 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:T.159, F:S.160, F:S.160, F:R.161, F:R.161, F:D.162, F:T.180, F:E.184, F:K.206, F:G.207, F:K.208, F:K.208, C:K.205 Salt bridges: F:R.161, C:R.161, C:R.161 pi-Cation interactions: F:K.206 ATP.22: 15 residues within 4Å: Chain F: I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.21 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:V.119, F:S.140, F:G.141, F:G.141, F:S.160, F:T.225, F:D.226 Salt bridges: F:K.134, F:K.208, F:K.208 pi-Stacking: F:F.139, F:F.139 ATP.25: 15 residues within 4Å: Chain B: R.161, K.205 Chain G: I.157, T.159, S.160, R.161, D.162, T.180, E.184, V.186, K.206, G.207, K.208 Ligands: ATP.5, ATP.26 14 PLIP interactions: 10 interactions with chain G, 4 interactions with chain B Hydrogen bonds: G:T.159, G:S.160, G:R.161, G:R.161, G:D.162, G:T.180, G:G.207, G:K.208, G:K.208, B:K.205 Salt bridges: G:R.161, B:R.161, B:R.161, B:R.161 ATP.26: 15 residues within 4Å: Chain G: I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.25 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:V.119, G:S.140, G:G.141, G:G.141, G:S.160, G:S.160, G:K.208, G:T.225, G:T.225, G:T.225, G:D.226 Salt bridges: G:K.134, G:K.208, G:K.208 pi-Stacking: G:F.139, G:F.139 ATP.29: 15 residues within 4Å: Chain A: R.161, K.205 Chain H: I.157, T.159, S.160, R.161, D.162, T.180, E.184, V.186, K.206, G.207, K.208 Ligands: ATP.1, ATP.30 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain H Hydrogen bonds: A:K.205, H:T.159, H:S.160, H:R.161, H:R.161, H:D.162, H:T.180, H:G.207, H:K.208, H:K.208 Salt bridges: A:R.161, A:R.161, A:R.161, H:R.161 ATP.30: 15 residues within 4Å: Chain H: I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.29 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:V.119, H:S.140, H:G.141, H:G.141, H:S.160, H:T.225, H:D.226 Salt bridges: H:K.134, H:K.208, H:K.208 pi-Stacking: H:F.139, H:F.139

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 21 residues within 4Å: Chain A: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.68, A:S.68, A:R.322, A:S.329, A:S.329, A:D.364, A:G.366, A:I.367, A:G.387, A:S.388, A:S.388, A:M.414, A:G.415, A:S.416, A:Q.441 IMP.7: 22 residues within 4Å: Chain B: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.68, B:S.68, B:R.322, B:S.329, B:S.329, B:D.364, B:G.366, B:I.367, B:G.387, B:S.388, B:S.388, B:M.414, B:G.415, B:S.416, B:Q.441 IMP.11: 21 residues within 4Å: Chain C: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.12 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.68, C:S.68, C:R.322, C:S.329, C:D.364, C:G.366, C:G.387, C:S.388, C:M.414, C:G.415, C:S.416, C:Q.441 IMP.15: 21 residues within 4Å: Chain D: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.68, D:S.68, D:R.322, D:S.329, D:S.329, D:D.364, D:G.366, D:I.367, D:G.387, D:S.388, D:S.388, D:M.414, D:G.415, D:S.416, D:Q.441 IMP.19: 21 residues within 4Å: Chain E: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.20 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.68, E:S.68, E:R.322, E:S.329, E:S.329, E:D.364, E:G.366, E:I.367, E:G.387, E:S.388, E:S.388, E:Y.411, E:M.414, E:G.415, E:S.416, E:Q.441 IMP.23: 21 residues within 4Å: Chain F: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.24 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.68, F:S.68, F:R.322, F:S.329, F:S.329, F:D.364, F:G.366, F:I.367, F:G.387, F:S.388, F:S.388, F:Y.411, F:M.414, F:G.415, F:S.416, F:Q.441 IMP.27: 21 residues within 4Å: Chain G: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.28 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:S.68, G:S.68, G:R.322, G:S.329, G:S.329, 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:S.416, G:Q.441 IMP.31: 22 residues within 4Å: Chain H: S.68, M.70, R.322, G.328, S.329, I.330, C.331, D.364, G.365, G.366, I.367, M.385, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.32 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:S.68, H:S.68, H:R.322, H:S.329, H:S.329, H:D.364, H:G.366, H:I.367, H:G.387, H:S.388, H:S.388, H:Y.411, H:M.414, H:G.415, H:S.416, H:Q.441

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

NAD.4: 19 residues within 4Å: Chain A: H.93, T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Chain D: I.45, H.466, Q.469 Ligands: IMP.3 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Q.441 Hydrogen bonds: A:T.252, A:T.252, A:R.253, A:R.253, A:D.274, A:S.276, A:G.324, A:G.326, A:Q.441, D:H.466, D:Q.469 pi-Stacking: A:Y.282, A:Y.282 pi-Cation interactions: A:R.253, A:R.253 NAD.8: 18 residues within 4Å: Chain A: I.45, H.466, Q.469 Chain B: T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Ligands: IMP.7 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:Q.469, B:T.252, B:T.252, B:R.253, B:R.253, B:D.274, B:S.276, B:G.324, B:G.326, B:Q.441 Hydrophobic interactions: B:Q.441 pi-Stacking: B:Y.282, B:Y.282 pi-Cation interactions: B:R.253, B:R.253 NAD.12: 17 residues within 4Å: Chain B: I.45, Q.469 Chain C: T.252, R.253, D.274, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, M.420, Q.441 Ligands: IMP.11 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.441 Hydrogen bonds: C:T.252, C:T.252, C:R.253, C:R.253, C:D.274, C:S.276, C:G.324, C:G.326, C:Q.441, B:Q.469 pi-Stacking: C:Y.282, C:Y.282 pi-Cation interactions: C:R.253, C:R.253 NAD.16: 18 residues within 4Å: Chain C: I.45, H.466, Q.469 Chain D: T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Ligands: IMP.15 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.441 Hydrogen bonds: D:T.252, D:T.252, D:R.253, D:R.253, D:D.274, D:S.276, D:G.324, D:G.326, C:H.466, C:Q.469 pi-Stacking: D:Y.282, D:Y.282 pi-Cation interactions: D:R.253, D:R.253 NAD.20: 17 residues within 4Å: Chain E: T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Chain H: I.45, Q.469 Ligands: IMP.19 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:Q.441 Hydrogen bonds: E:T.252, E:R.253, E:R.253, E:D.274, E:S.276, E:G.324, E:G.326, H:H.466, H:Q.469 pi-Stacking: E:Y.282, E:Y.282 pi-Cation interactions: E:R.253, E:R.253 NAD.24: 18 residues within 4Å: Chain E: I.45, H.466, Q.469 Chain F: T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Ligands: IMP.23 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Q.441 Hydrogen bonds: F:T.252, F:R.253, F:R.253, F:D.274, F:S.276, F:G.324, F:G.326, E:Q.469, E:Q.469 pi-Stacking: F:Y.282, F:Y.282 pi-Cation interactions: F:R.253, F:R.253 NAD.28: 18 residues within 4Å: Chain F: I.45, H.466, Q.469 Chain G: T.252, R.253, D.274, S.275, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Ligands: IMP.27 14 PLIP interactions: 12 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:Q.441 Hydrogen bonds: G:T.252, G:R.253, G:R.253, G:D.274, G:S.276, G:G.324, G:G.326, F:H.466, F:Q.469 pi-Stacking: G:Y.282, G:Y.282 pi-Cation interactions: G:R.253, G:R.253 NAD.32: 15 residues within 4Å: Chain G: I.45, Q.469 Chain H: T.252, R.253, D.274, S.276, Y.282, N.303, G.324, M.325, G.326, T.333, M.414, Q.441 Ligands: IMP.31 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Q.441 Hydrogen bonds: H:R.253, H:R.253, H:D.274, H:S.276, H:Y.282, H:G.324, H:G.326, G:Q.469, G:Q.469 pi-Stacking: H:Y.282, H:Y.282 pi-Cation interactions: H:R.253

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

Isoform 5 of 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

Isoform 5 of Inosine-5'-monophosphate dehydrogenase 1

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