SMTL ID : 8u7m.1

Human retinal variant phosphomimetic IMPDH1(595)-S477D free octamer bound by GTP, ATP, IMP, and NAD+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

GTP.1: 15 residues within 4Å: Chain A: K.160, F.161, Q.163, I.166, D.168, P.169, V.170, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.163, A:V.170, A:S.191, A:K.259, A:K.259, A:T.276, A:D.277 Salt bridges: A:K.259 pi-Stacking: A:F.190, A:F.190 pi-Cation interactions: A:F.190 GTP.2: 10 residues within 4Å: Chain A: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.164, A:N.249, A:N.249, A:N.281, A:K.289 Salt bridges: A:D.277, A:K.289, A:K.293 GTP.6: 16 residues within 4Å: Chain B: K.160, F.161, Q.163, I.166, D.168, P.169, V.170, F.190, S.191, G.192, T.210, K.259, A.274, T.276, D.277 Ligands: ATP.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.160, B:Q.163, B:G.164, B:V.170, B:S.191, B:K.259, B:K.259, B:T.276, B:D.277 Salt bridges: B:K.259 pi-Stacking: B:F.190 pi-Cation interactions: B:F.190 GTP.7: 10 residues within 4Å: Chain B: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.249, B:N.249, B:N.281, B:K.289 Salt bridges: B:D.277, B:K.289, B:K.293 GTP.11: 15 residues within 4Å: Chain C: K.160, F.161, E.162, Q.163, I.166, D.168, P.169, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.160, C:Q.163, C:G.164, C:S.191, C:K.259, C:K.259, C:T.276, C:D.277 Salt bridges: C:K.259 GTP.12: 10 residues within 4Å: Chain C: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.164, C:N.249, C:N.249, C:N.281, C:K.289 Salt bridges: C:D.277, C:K.289, C:K.293 GTP.16: 15 residues within 4Å: Chain D: K.160, F.161, E.162, Q.163, I.166, D.168, P.169, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.18 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.160, D:Q.163, D:G.164, D:S.191, D:K.259, D:K.259, D:T.276, D:D.277 Salt bridges: D:K.259 GTP.17: 10 residues within 4Å: Chain D: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.164, D:N.249, D:N.249, D:N.281, D:K.289 Salt bridges: D:D.277, D:K.289, D:K.293 GTP.21: 16 residues within 4Å: Chain E: K.160, F.161, E.162, Q.163, G.164, I.166, D.168, P.169, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.23 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:K.160, E:Q.163, E:G.164, E:V.170, E:S.191, E:K.259, E:K.259, E:T.276, E:D.277 Salt bridges: E:K.259 GTP.22: 10 residues within 4Å: Chain E: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.164, E:N.249, E:N.249, E:N.281, E:K.289 Salt bridges: E:D.277, E:K.289, E:K.293 GTP.26: 15 residues within 4Å: Chain F: K.160, F.161, Q.163, I.166, D.168, P.169, V.170, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.28 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Q.163, F:V.170, F:S.191, F:K.259, F:K.259, F:T.276, F:D.277 Salt bridges: F:K.259 pi-Stacking: F:F.190, F:F.190 pi-Cation interactions: F:F.190 GTP.27: 10 residues within 4Å: Chain F: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.164, F:N.249, F:N.249, F:N.281, F:K.289 Salt bridges: F:D.277, F:K.289, F:K.293 GTP.31: 16 residues within 4Å: Chain G: K.160, F.161, E.162, Q.163, G.164, I.166, D.168, P.169, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.33 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:K.160, G:Q.163, G:G.164, G:V.170, G:S.191, G:G.192, G:T.276, G:D.277 Salt bridges: G:K.259, G:K.259, G:K.259 GTP.32: 10 residues within 4Å: Chain G: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.164, G:N.249, G:N.249, G:N.281, G:K.289 Salt bridges: G:D.277, G:K.289, G:K.293 GTP.36: 16 residues within 4Å: Chain H: K.160, F.161, E.162, Q.163, G.164, I.166, D.168, P.169, F.190, S.191, G.192, T.210, K.259, T.276, D.277 Ligands: ATP.38 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:K.160, H:Q.163, H:G.164, H:V.170, H:S.191, H:G.192, H:T.276, H:D.277 Salt bridges: H:K.259, H:K.259, H:K.259 GTP.37: 10 residues within 4Å: Chain H: E.162, G.164, L.245, K.246, N.249, D.277, L.278, N.281, K.289, K.293 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:G.164, H:N.249, H:N.249, H:N.281, H:K.289 Salt bridges: H:D.277, H:K.289, H:K.293

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

ATP.3: 13 residues within 4Å: Chain A: I.208, T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259 Chain E: R.212 Ligands: GTP.1, ATP.23 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:T.210, A:T.210, A:S.211, A:R.212, A:T.231, A:V.237, A:V.237, A:G.258, E:R.212 Salt bridges: A:R.212, A:R.212, E:R.212, E:K.279 ATP.8: 13 residues within 4Å: Chain B: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259, P.261 Chain H: R.212 Ligands: GTP.6, ATP.38 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain H Hydrogen bonds: B:T.210, B:T.210, B:S.211, B:R.212, B:T.231, B:V.237, B:V.237, B:G.258, H:R.212 Salt bridges: B:R.212, B:R.212, H:R.212, H:K.279 ATP.13: 13 residues within 4Å: Chain C: T.210, R.212, D.213, T.231, E.235, L.236, V.237, K.257, G.258, K.259 Chain G: R.212 Ligands: GTP.11, ATP.33 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain G Hydrogen bonds: C:T.210, C:T.210, C:S.211, C:R.212, C:T.231, C:V.237, C:V.237, C:G.258, G:R.212 Salt bridges: C:R.212, C:R.212, G:R.212, G:K.279 ATP.18: 13 residues within 4Å: Chain D: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259, P.261 Chain F: R.212 Ligands: GTP.16, ATP.28 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:T.210, D:T.210, D:S.211, D:R.212, D:T.231, D:V.237, D:V.237, D:G.258, F:R.212 Salt bridges: D:R.212, D:R.212, F:R.212, F:K.279 ATP.23: 13 residues within 4Å: Chain A: R.212 Chain E: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259, P.261 Ligands: ATP.3, GTP.21 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:T.210, E:T.210, E:S.211, E:R.212, E:T.231, E:V.237, E:V.237, E:G.258, A:R.212 Salt bridges: E:R.212, E:R.212, A:R.212, A:K.279 ATP.28: 12 residues within 4Å: Chain D: R.212 Chain F: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259 Ligands: ATP.18, GTP.26 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:T.210, F:T.210, F:S.211, F:R.212, F:T.231, F:V.237, F:V.237, F:G.258, D:R.212 Salt bridges: F:R.212, F:R.212, D:R.212, D:K.279 ATP.33: 13 residues within 4Å: Chain C: R.212 Chain G: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259, P.261 Ligands: ATP.13, GTP.31 16 PLIP interactions: 13 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:T.210, G:T.210, G:S.211, G:R.212, G:T.231, G:V.237, G:V.237, G:G.258, G:K.259, C:R.212 Salt bridges: G:R.212, G:R.212, G:K.259, G:K.259, C:R.212, C:K.279 ATP.38: 13 residues within 4Å: Chain B: R.212 Chain H: T.210, R.212, D.213, E.235, L.236, V.237, K.257, G.258, K.259, P.261 Ligands: ATP.8, GTP.36 16 PLIP interactions: 3 interactions with chain B, 13 interactions with chain H Hydrogen bonds: B:R.212, H:T.210, H:T.210, H:S.211, H:R.212, H:T.231, H:V.237, H:V.237, H:G.258, H:K.259 Salt bridges: B:R.212, B:K.279, H:R.212, H:R.212, H:K.259, H:K.259

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 15 residues within 4Å: Chain A: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.119, A:R.373, A:S.380, A:D.415, A:G.417, A:G.438, A:S.439, A:S.439, A:Q.492 IMP.9: 15 residues within 4Å: Chain B: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.119, B:R.373, B:S.380, B:D.415, B:G.417, B:G.438, B:S.439, B:S.439, B:Q.492 IMP.14: 15 residues within 4Å: Chain C: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.119, C:R.373, C:S.380, C:D.415, C:G.416, C:G.417, C:G.438, C:S.439, C:S.439, C:Q.492 IMP.19: 15 residues within 4Å: Chain D: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.119, D:R.373, D:S.380, D:D.415, D:G.417, D:G.438, D:S.439, D:S.439, D:Q.492 IMP.24: 15 residues within 4Å: Chain E: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.25 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.119, E:R.373, E:S.380, E:D.415, E:G.417, E:G.438, E:S.439, E:Q.492 IMP.29: 15 residues within 4Å: Chain F: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.30 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.119, F:R.373, F:S.380, F:D.415, F:G.417, F:G.438, F:S.439, F:Q.492 IMP.34: 15 residues within 4Å: Chain G: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.35 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.119, G:R.373, G:S.380, G:D.415, G:G.417, G:G.438, G:S.439, G:Q.492 IMP.39: 15 residues within 4Å: Chain H: S.119, M.121, R.373, G.379, S.380, C.382, D.415, G.416, G.417, M.437, G.438, S.439, Q.492, G.493 Ligands: NAD.40 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.119, H:R.373, H:S.380, H:D.415, H:G.417, H:G.438, H:S.439, H:Q.492

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

NAD.5: 18 residues within 4Å: Chain A: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain B: I.96, A.97, H.517, Q.520 Ligands: IMP.4 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.303, A:R.304, A:R.304, A:S.326, A:S.326, A:S.327, A:N.354, A:G.375, A:G.377, A:Q.492, B:H.517, B:Q.520 Salt bridges: A:R.304 pi-Stacking: A:Y.333, A:Y.333 pi-Cation interactions: A:R.304, A:R.304 NAD.10: 17 residues within 4Å: Chain B: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain C: I.96, A.97, Q.520 Ligands: IMP.9 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.303, B:R.304, B:R.304, B:S.326, B:S.326, B:S.327, B:N.354, B:G.375, B:G.377, B:Q.492, C:Q.520 Salt bridges: B:R.304 pi-Cation interactions: B:R.304 NAD.15: 17 residues within 4Å: Chain C: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain D: I.96, A.97, Q.520 Ligands: IMP.14 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.303, C:R.304, C:R.304, C:S.326, C:S.326, C:S.327, C:N.354, C:G.375, C:G.377, C:Q.492, D:H.517, D:Q.520 Salt bridges: C:R.304 pi-Cation interactions: C:R.304 NAD.20: 16 residues within 4Å: Chain A: I.96, A.97, Q.520 Chain D: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384 Ligands: IMP.19 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.303, D:R.304, D:R.304, D:S.326, D:S.326, D:S.327, D:N.354, D:G.375, D:G.377, A:Q.520 Salt bridges: D:R.304 pi-Cation interactions: D:R.304 NAD.25: 18 residues within 4Å: Chain E: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain F: I.96, A.97, H.517, Q.520 Ligands: IMP.24 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.303, E:R.304, E:R.304, E:S.326, E:S.326, E:S.327, E:N.354, E:G.375, E:G.377, E:Q.492, F:H.517, F:Q.520 Salt bridges: E:R.304 pi-Stacking: E:Y.333, E:Y.333 pi-Cation interactions: E:R.304, E:R.304 NAD.30: 17 residues within 4Å: Chain F: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain G: I.96, A.97, Q.520 Ligands: IMP.29 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:T.303, F:R.304, F:R.304, F:S.326, F:S.326, F:S.327, F:N.354, F:G.375, F:G.377, F:Q.492, G:H.517, G:Q.520 Salt bridges: F:R.304 pi-Cation interactions: F:R.304 NAD.35: 17 residues within 4Å: Chain G: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Chain H: I.96, A.97, Q.520 Ligands: IMP.34 14 PLIP interactions: 2 interactions with chain H, 12 interactions with chain G Hydrogen bonds: H:H.517, H:Q.520, G:T.303, G:R.304, G:R.304, G:S.326, G:S.326, G:S.327, G:N.354, G:G.375, G:G.377, G:Q.492 Salt bridges: G:R.304 pi-Cation interactions: G:R.304 NAD.40: 17 residues within 4Å: Chain E: I.96, A.97, Q.520 Chain H: T.303, R.304, D.325, S.326, S.327, Y.333, N.354, G.375, M.376, G.377, C.382, T.384, Q.492 Ligands: IMP.39 14 PLIP interactions: 2 interactions with chain E, 12 interactions with chain H Hydrogen bonds: E:H.517, E:Q.520, H:T.303, H:R.304, H:R.304, H:S.326, H:S.326, H:S.327, H:N.354, H:G.375, H:G.377, H:Q.492 Salt bridges: H:R.304 pi-Cation interactions: H:R.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calise, S.J. et al., Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J.Cell Biol. (2024)

Release Date

2024-01-31

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