SMTL ID : 8u8o.1

Human retinal variant phosphomimetic IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+, octamer-centered

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Chain G: R.163, K.207 Ligands: ATP.2, ATP.25 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain G Hydrogen bonds: A:T.161, A:S.162, A:R.163, A:D.164, A:V.188, A:V.188, A:K.208, A:G.209, A:K.210, G:R.163, G:K.207, G:K.207 Salt bridges: A:R.163, G:R.163 ATP.2: 14 residues within 4Å: Chain A: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.121, A:S.142, A:G.143, A:G.143, A:S.162, A:S.162, A:K.210, A:T.227, A:T.227, A:D.228 Salt bridges: A:K.136, A:K.210, A:K.210 pi-Stacking: A:F.141, A:F.141 ATP.5: 16 residues within 4Å: Chain B: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Chain F: R.163, K.207 Ligands: ATP.6, ATP.21 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:T.161, B:S.162, B:R.163, B:D.164, B:V.188, B:V.188, B:K.208, B:G.209, B:K.210, F:R.163, F:K.207, F:K.207 Salt bridges: B:R.163, F:R.163 ATP.6: 14 residues within 4Å: Chain B: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:V.121, B:S.142, B:G.143, B:G.143, B:S.162, B:S.162, B:K.210, B:T.227, B:T.227, B:D.228 Salt bridges: B:K.136, B:K.210, B:K.210 pi-Stacking: B:F.141, B:F.141 ATP.9: 16 residues within 4Å: Chain C: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Chain E: R.163, K.207 Ligands: ATP.10, ATP.17 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:T.161, C:S.162, C:R.163, C:D.164, C:V.188, C:V.188, C:K.208, C:G.209, C:K.210, E:R.163, E:K.207, E:K.207 Salt bridges: C:R.163, E:R.163 ATP.10: 14 residues within 4Å: Chain C: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.9 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:V.121, C:S.142, C:G.143, C:G.143, C:S.162, C:S.162, C:K.210, C:T.227, C:T.227, C:D.228 Salt bridges: C:K.136, C:K.210, C:K.210 pi-Stacking: C:F.141, C:F.141 ATP.13: 16 residues within 4Å: Chain D: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Chain H: R.163, K.207 Ligands: ATP.14, ATP.29 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain H Hydrogen bonds: D:T.161, D:S.162, D:R.163, D:D.164, D:V.188, D:V.188, D:K.208, D:G.209, D:K.210, H:R.163, H:K.207, H:K.207 Salt bridges: D:R.163, H:R.163 ATP.14: 14 residues within 4Å: Chain D: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.13 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.121, D:S.142, D:G.143, D:G.143, D:S.162, D:S.162, D:K.210, D:T.227, D:T.227, D:D.228 Salt bridges: D:K.136, D:K.210, D:K.210 pi-Stacking: D:F.141, D:F.141 ATP.17: 16 residues within 4Å: Chain C: R.163, K.207 Chain E: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Ligands: ATP.9, ATP.18 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:T.161, E:S.162, E:R.163, E:D.164, E:V.188, E:V.188, E:K.208, E:G.209, E:K.210, C:K.207, C:K.207 Salt bridges: E:R.163, C:R.163, C:R.163 ATP.18: 14 residues within 4Å: Chain E: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.17 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:V.121, E:S.142, E:G.143, E:G.143, E:S.162, E:S.162, E:K.210, E:T.227, E:T.227, E:D.228, E:D.228 Salt bridges: E:K.136, E:K.210, E:K.210 pi-Stacking: E:F.141, E:F.141 ATP.21: 16 residues within 4Å: Chain B: R.163, K.207 Chain F: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Ligands: ATP.5, ATP.22 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:T.161, F:S.162, F:R.163, F:D.164, F:V.188, F:V.188, F:K.208, F:G.209, F:K.210, B:K.207, B:K.207 Salt bridges: F:R.163, B:R.163, B:R.163 ATP.22: 14 residues within 4Å: Chain F: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.21 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:V.121, F:S.142, F:G.143, F:G.143, F:S.162, F:S.162, F:K.210, F:T.227, F:T.227, F:D.228, F:D.228 Salt bridges: F:K.136, F:K.210, F:K.210 pi-Stacking: F:F.141, F:F.141 ATP.25: 16 residues within 4Å: Chain A: R.163, K.207 Chain G: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Ligands: ATP.1, ATP.26 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain G Hydrogen bonds: A:K.207, A:K.207, G:T.161, G:S.162, G:R.163, G:D.164, G:V.188, G:V.188, G:K.208, G:G.209, G:K.210 Salt bridges: A:R.163, A:R.163, G:R.163 ATP.26: 14 residues within 4Å: Chain G: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.25 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:V.121, G:S.142, G:G.143, G:G.143, G:S.162, G:S.162, G:K.210, G:T.227, G:T.227, G:D.228, G:D.228 Salt bridges: G:K.136, G:K.210, G:K.210 pi-Stacking: G:F.141, G:F.141 ATP.29: 16 residues within 4Å: Chain D: R.163, K.207 Chain H: I.159, T.161, S.162, R.163, D.164, T.182, E.186, V.188, K.208, G.209, K.210, P.212 Ligands: ATP.13, ATP.30 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain D Hydrogen bonds: H:T.161, H:S.162, H:R.163, H:D.164, H:V.188, H:V.188, H:K.208, H:G.209, H:K.210, D:K.207, D:K.207 Salt bridges: H:R.163, D:R.163, D:R.163 ATP.30: 14 residues within 4Å: Chain H: I.117, P.120, V.121, K.136, F.141, S.142, G.143, P.145, S.162, K.210, A.225, T.227, D.228 Ligands: ATP.29 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:V.121, H:S.142, H:G.143, H:G.143, H:S.162, H:S.162, H:K.210, H:T.227, H:T.227, H:D.228 Salt bridges: H:K.136, H:K.210, H:K.210 pi-Stacking: H:F.141, H:F.141

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 22 residues within 4Å: Chain A: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:R.324, A:S.331, A:S.331, A:D.366, A:G.368, A:G.389, A:S.390, A:M.416, A:G.417, A:S.418, A:Q.443 IMP.7: 22 residues within 4Å: Chain B: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.70, B:S.70, B:R.324, B:S.331, B:S.331, B:D.366, B:G.368, B:G.389, B:S.390, B:M.416, B:G.417, B:S.418, B:Q.443 IMP.11: 22 residues within 4Å: Chain C: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.70, C:S.70, C:R.324, C:S.331, C:S.331, C:D.366, C:G.368, C:G.389, C:S.390, C:M.416, C:G.417, C:S.418, C:Q.443 IMP.15: 22 residues within 4Å: Chain D: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.70, D:S.70, D:R.324, D:S.331, D:S.331, D:D.366, D:G.368, D:G.389, D:S.390, D:M.416, D:G.417, D:S.418, D:Q.443 IMP.19: 22 residues within 4Å: Chain E: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.70, E:S.70, E:R.324, E:S.331, E:S.331, E:D.366, E:G.368, E:G.389, E:S.390, E:Y.413, E:M.416, E:G.417, E:S.418, E:Q.443 IMP.23: 22 residues within 4Å: Chain F: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.70, F:S.70, F:R.324, F:S.331, F:S.331, F:D.366, F:G.368, F:G.389, F:S.390, F:Y.413, F:M.416, F:G.417, F:S.418, F:Q.443 IMP.27: 22 residues within 4Å: Chain G: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.28 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.70, G:S.70, G:R.324, G:S.331, G:S.331, G:D.366, G:G.368, G:G.389, G:S.390, G:Y.413, G:M.416, G:G.417, G:S.418, G:Q.443 IMP.31: 22 residues within 4Å: Chain H: S.70, M.72, R.324, G.330, S.331, I.332, C.333, T.335, D.366, G.367, G.368, M.387, G.389, S.390, Y.413, G.415, M.416, G.417, S.418, Q.443, G.444 Ligands: NAD.32 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.70, H:S.70, H:R.324, H:S.331, H:S.331, H:D.366, H:G.368, H:G.389, H:S.390, H:Y.413, H:M.416, H:G.417, H:S.418, H:Q.443

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

NAD.4: 16 residues within 4Å: Chain A: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Chain D: Q.471 Ligands: IMP.3 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:T.254, A:T.254, A:R.255, A:D.276, A:S.278, A:G.326, A:G.328, D:Q.471, D:Q.471 pi-Stacking: A:Y.284, A:Y.284 pi-Cation interactions: A:R.255, A:R.255 NAD.8: 16 residues within 4Å: Chain A: Q.471 Chain B: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.254, B:T.254, B:R.255, B:D.276, B:S.278, B:G.326, B:G.328, A:Q.471, A:Q.471 pi-Stacking: B:Y.284, B:Y.284 pi-Cation interactions: B:R.255, B:R.255 NAD.12: 16 residues within 4Å: Chain B: Q.471 Chain C: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.11 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.254, C:T.254, C:R.255, C:D.276, C:S.278, C:G.326, C:G.328, B:Q.471, B:Q.471 pi-Stacking: C:Y.284, C:Y.284 pi-Cation interactions: C:R.255, C:R.255 NAD.16: 16 residues within 4Å: Chain C: Q.471 Chain D: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.15 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.254, D:T.254, D:R.255, D:D.276, D:S.278, D:G.326, D:G.328, C:Q.471, C:Q.471 pi-Stacking: D:Y.284, D:Y.284 pi-Cation interactions: D:R.255, D:R.255 NAD.20: 16 residues within 4Å: Chain E: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Chain H: Q.471 Ligands: IMP.19 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:T.254, E:R.255, E:D.276, E:S.278, E:G.326, E:G.328, H:Q.471, H:Q.471 pi-Stacking: E:Y.284, E:Y.284 pi-Cation interactions: E:R.255, E:R.255 NAD.24: 16 residues within 4Å: Chain E: Q.471 Chain F: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.23 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:T.254, F:R.255, F:D.276, F:S.278, F:G.326, F:G.328, E:Q.471, E:Q.471 pi-Stacking: F:Y.284, F:Y.284 pi-Cation interactions: F:R.255, F:R.255 NAD.28: 16 residues within 4Å: Chain F: Q.471 Chain G: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.27 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:T.254, G:R.255, G:D.276, G:S.278, G:G.326, G:G.328, F:Q.471, F:Q.471 pi-Stacking: G:Y.284, G:Y.284 pi-Cation interactions: G:R.255, G:R.255 NAD.32: 16 residues within 4Å: Chain G: Q.471 Chain H: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, T.335, M.416, G.417, Q.443 Ligands: IMP.31 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:T.254, H:R.255, H:D.276, H:S.278, H:G.326, H:G.328, G:Q.471, G:Q.471 pi-Stacking: H:Y.284, H:Y.284 pi-Cation interactions: H:R.255, H:R.255

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

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