SMTL ID : 8u7v.1

Human retinal variant phosphomimetic IMPDH1(546)-S477D filament bound by GTP, ATP, IMP, and 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: 7 residues within 4Å: Chain A: E.113, G.115, N.200, D.228, N.232, K.240, K.244 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.115, A:N.200, A:N.232, A:K.240 Salt bridges: A:K.240, A:K.240, A:K.244 GTP.5: 14 residues within 4Å: Chain A: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:F.112, A:F.141, A:S.142, A:S.142, A:G.143, A:K.210, A:K.231 Salt bridges: A:K.111, A:K.111, A:K.111 pi-Stacking: A:F.141 pi-Cation interactions: A:K.210 GTP.6: 7 residues within 4Å: Chain B: E.113, G.115, N.200, D.228, N.232, K.240, K.244 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.115, B:N.200, B:N.232, B:K.240 Salt bridges: B:K.240, B:K.240, B:K.244 GTP.10: 14 residues within 4Å: Chain B: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.9 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:F.112, B:F.141, B:S.142, B:S.142, B:G.143, B:K.210, B:K.231 Salt bridges: B:K.111, B:K.111, B:K.111 pi-Stacking: B:F.141 pi-Cation interactions: B:K.210 GTP.11: 7 residues within 4Å: Chain C: E.113, G.115, N.200, D.228, N.232, K.240, K.244 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.115, C:N.200, C:N.232, C:K.240 Salt bridges: C:K.240, C:K.240, C:K.244 GTP.15: 14 residues within 4Å: Chain C: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.14 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.112, C:F.141, C:S.142, C:S.142, C:G.143, C:K.210, C:K.231 Salt bridges: C:K.111, C:K.111, C:K.111 pi-Stacking: C:F.141 pi-Cation interactions: C:K.210 GTP.16: 7 residues within 4Å: Chain D: E.113, G.115, N.200, D.228, N.232, K.240, K.244 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.115, D:N.200, D:N.232, D:K.240 Salt bridges: D:K.240, D:K.240, D:K.244 GTP.20: 14 residues within 4Å: Chain D: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.19 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:F.112, D:F.141, D:S.142, D:S.142, D:G.143, D:K.210, D:K.231 Salt bridges: D:K.111, D:K.111, D:K.111 pi-Stacking: D:F.141 pi-Cation interactions: D:K.210 GTP.21: 7 residues within 4Å: Chain E: E.113, G.115, N.200, D.228, N.232, K.240, K.244 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.113, E:G.115, E:N.200, E:N.232, E:K.240 Salt bridges: E:K.240, E:K.240, E:K.244 GTP.25: 14 residues within 4Å: Chain E: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.24 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:F.112, E:F.141, E:S.142, E:S.142, E:G.143, E:K.210, E:K.231 Salt bridges: E:K.111, E:K.111, E:K.111 pi-Stacking: E:F.141 pi-Cation interactions: E:K.210 GTP.26: 7 residues within 4Å: Chain F: E.113, G.115, N.200, D.228, N.232, K.240, K.244 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.113, F:G.115, F:N.200, F:N.232, F:K.240 Salt bridges: F:K.240, F:K.240, F:K.244 GTP.30: 14 residues within 4Å: Chain F: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.29 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:F.112, F:F.141, F:S.142, F:S.142, F:G.143, F:K.210, F:K.231 Salt bridges: F:K.111, F:K.111, F:K.111 pi-Stacking: F:F.141 pi-Cation interactions: F:K.210 GTP.31: 7 residues within 4Å: Chain G: E.113, G.115, N.200, D.228, N.232, K.240, K.244 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.113, G:G.115, G:N.200, G:N.232, G:K.240 Salt bridges: G:K.240, G:K.240, G:K.244 GTP.35: 14 residues within 4Å: Chain G: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.34 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:F.112, G:F.141, G:S.142, G:S.142, G:G.143, G:K.210, G:K.231 Salt bridges: G:K.111, G:K.111, G:K.111 pi-Stacking: G:F.141 pi-Cation interactions: G:K.210 GTP.36: 7 residues within 4Å: Chain H: E.113, G.115, N.200, D.228, N.232, K.240, K.244 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:E.113, H:G.115, H:N.200, H:N.232, H:K.240 Salt bridges: H:K.240, H:K.240, H:K.244 GTP.40: 14 residues within 4Å: Chain H: K.111, F.112, Q.114, I.117, H.139, F.141, S.142, G.143, S.162, K.210, T.227, D.228, K.231 Ligands: ATP.39 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:F.112, H:F.141, H:S.142, H:S.142, H:G.143, H:K.210, H:K.231 Salt bridges: H:K.111, H:K.111, H:K.111 pi-Stacking: H:F.141 pi-Cation interactions: H:K.210

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

NAD.2: 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, C.333, T.335, M.416, Q.443 Chain B: Q.471 Ligands: IMP.3 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Q.471, A:T.254, A:R.255, A:D.276, A:S.278, A:N.305, A:G.328 Hydrophobic interactions: A:T.335 pi-Stacking: A:Y.284, A:Y.284 pi-Cation interactions: A:R.255, A:R.255 NAD.7: 16 residues within 4Å: Chain B: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Chain C: Q.471 Ligands: IMP.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.335 Hydrogen bonds: B:T.254, B:R.255, B:D.276, B:S.278, B:N.305, B:G.328, C: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 C: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Chain D: Q.471 Ligands: IMP.13 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.335 Hydrogen bonds: C:T.254, C:R.255, C:D.276, C:S.278, C:N.305, C:G.328, D:Q.471 pi-Stacking: C:Y.284, C:Y.284 pi-Cation interactions: C:R.255, C:R.255 NAD.17: 16 residues within 4Å: Chain A: Q.471 Chain D: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Ligands: IMP.18 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:Q.471, D:T.254, D:R.255, D:D.276, D:S.278, D:N.305, D:G.328 Hydrophobic interactions: D:T.335 pi-Stacking: D:Y.284, D:Y.284 pi-Cation interactions: D:R.255, D:R.255 NAD.22: 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, C.333, T.335, M.416, Q.443 Chain F: Q.471 Ligands: IMP.23 13 PLIP interactions: 1 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:Q.471, E:T.254, E:T.254, E:R.255, E:D.276, E:S.278, E:N.305, E:G.328 Hydrophobic interactions: E:T.335 pi-Stacking: E:Y.284, E:Y.284 pi-Cation interactions: E:R.255, E:R.255 NAD.27: 16 residues within 4Å: Chain F: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Chain G: Q.471 Ligands: IMP.28 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:T.335 Hydrogen bonds: F:T.254, F:T.254, F:R.255, F:D.276, F:S.278, F:N.305, F:G.328, G:Q.471 pi-Stacking: F:Y.284, F:Y.284 pi-Cation interactions: F:R.255, F:R.255 NAD.32: 16 residues within 4Å: Chain G: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Chain H: Q.471 Ligands: IMP.33 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:T.335 Hydrogen bonds: G:T.254, G:T.254, G:R.255, G:D.276, G:S.278, G:N.305, G:G.328, H:Q.471 pi-Stacking: G:Y.284, G:Y.284 pi-Cation interactions: G:R.255, G:R.255 NAD.37: 16 residues within 4Å: Chain E: Q.471 Chain H: T.254, R.255, D.276, S.277, S.278, Y.284, N.305, G.326, M.327, G.328, C.333, T.335, M.416, Q.443 Ligands: IMP.38 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:T.335 Hydrogen bonds: H:T.254, H:T.254, H:R.255, H:D.276, H:S.278, H:N.305, H:G.328, E:Q.471 pi-Stacking: H:Y.284, H:Y.284 pi-Cation interactions: H:R.255, H:R.255

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 16 residues within 4Å: Chain A: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.324, A:S.331, A:D.366, A:D.366, A:G.367, A:G.368, A:G.389, A:S.390, A:M.416, A:G.417, A:Q.443 IMP.8: 16 residues within 4Å: Chain B: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.324, B:S.331, B:D.366, B:D.366, B:G.367, B:G.368, B:G.389, B:S.390, B:M.416, B:G.417, B:Q.443 IMP.13: 16 residues within 4Å: Chain C: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.324, C:S.331, C:D.366, C:G.367, C:G.368, C:G.389, C:S.390, C:M.416, C:G.417, C:Q.443 IMP.18: 16 residues within 4Å: Chain D: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.17 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.324, D:S.331, D:D.366, D:D.366, D:G.367, D:G.368, D:G.389, D:S.390, D:M.416, D:G.417, D:Q.443 IMP.23: 16 residues within 4Å: Chain E: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.22 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.324, E:S.331, E:D.366, E:G.367, E:G.368, E:G.389, E:S.390, E:M.416, E:G.417, E:Q.443 IMP.28: 16 residues within 4Å: Chain F: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.27 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:R.324, F:S.331, F:D.366, F:G.367, F:G.368, F:G.389, F:S.390, F:M.416, F:G.417, F:Q.443 IMP.33: 16 residues within 4Å: Chain G: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.32 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:R.324, G:S.331, G:D.366, G:G.367, G:G.368, G:G.389, G:S.390, G:M.416, G:G.417, G:Q.443 IMP.38: 16 residues within 4Å: Chain H: M.72, R.324, G.330, S.331, C.333, T.335, D.366, G.367, G.368, G.389, S.390, G.415, M.416, G.417, Q.443 Ligands: NAD.37 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:R.324, H:S.331, H:G.367, H:G.368, H:G.389, H:S.390, H:M.416, H:G.417, H:Q.443

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

ATP.4: 15 residues within 4Å: Chain A: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.161, A:S.162, A:D.164, A:V.188, A:V.188, A:G.209, A:K.210 Salt bridges: A:R.163 ATP.9: 15 residues within 4Å: Chain B: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.161, B:S.162, B:D.164, B:V.188, B:V.188, B:G.209, B:K.210 Salt bridges: B:R.163 ATP.14: 15 residues within 4Å: Chain C: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.15 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.161, C:S.162, C:D.164, C:V.188, C:V.188, C:G.209, C:K.210 Salt bridges: C:R.163, C:K.210 ATP.19: 15 residues within 4Å: Chain D: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.20 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.161, D:S.162, D:D.164, D:V.188, D:V.188, D:G.209, D:K.210 Salt bridges: D:R.163 ATP.24: 15 residues within 4Å: Chain E: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.25 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.162, E:D.164, E:V.188, E:V.188, E:G.209, E:K.210 Salt bridges: E:R.163 ATP.29: 15 residues within 4Å: Chain F: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.30 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.162, F:D.164, F:V.188, F:V.188, F:G.209, F:K.210 Salt bridges: F:R.163 ATP.34: 15 residues within 4Å: Chain G: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.35 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:S.162, G:D.164, G:V.188, G:V.188, G:G.209, G:K.210 Salt bridges: G:R.163 ATP.39: 15 residues within 4Å: Chain H: S.142, I.159, T.161, S.162, R.163, D.164, T.182, E.186, L.187, V.188, K.208, G.209, K.210, P.212 Ligands: GTP.40 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.162, H:D.164, H:V.188, H:V.188, H:G.209, H:K.210 Salt bridges: H:R.163, H:K.210

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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