SMTL ID : 7rfi.1

HUMAN RETINAL VARIANT IMPDH1(595) 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: 10 residues within 4Å: Chain A: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.187, A:T.300, A:D.301, A:D.301 GTP.2: 17 residues within 4Å: Chain A: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.187, A:Q.187, A:N.305, A:Y.308, A:P.309, A:K.313 Salt bridges: A:K.137, A:K.137, A:K.313, A:K.313, A:K.317, A:K.317 GTP.5: 10 residues within 4Å: Chain B: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.187, B:T.300, B:D.301, B:D.301 GTP.6: 16 residues within 4Å: Chain B: K.137, E.186, Q.187, G.188, L.269, A.272, N.273, I.297, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.187, B:G.188, B:N.305, B:N.305, B:Y.308, B:P.309, B:K.313 Salt bridges: B:K.137, B:K.313, B:K.313, B:K.317, B:K.317 GTP.9: 11 residues within 4Å: Chain C: K.184, F.185, E.186, Q.187, I.190, D.192, P.193, A.298, T.300, D.301, K.304 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.187, C:Q.187, C:T.300, C:D.301, C:D.301 GTP.10: 18 residues within 4Å: Chain C: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, A.298, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.187, C:Q.187, C:N.305, C:Y.308, C:P.309, C:A.311, C:K.313 Salt bridges: C:K.137, C:K.137, C:K.313, C:K.313, C:K.317 GTP.13: 11 residues within 4Å: Chain D: K.184, F.185, E.186, Q.187, I.190, P.193, I.296, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.187, D:T.300, D:D.301, D:D.301 GTP.14: 18 residues within 4Å: Chain D: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, A.298, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.187, D:Q.187, D:N.273, D:N.305, D:Y.308, D:Y.308, D:K.313 Salt bridges: D:K.137, D:K.137, D:K.313, D:K.313, D:K.317 GTP.17: 10 residues within 4Å: Chain E: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.187, E:T.300, E:T.300, E:D.301, E:D.301, E:D.301 GTP.18: 17 residues within 4Å: Chain E: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:E.186, E:Q.187, E:G.188, E:N.273, E:N.305, E:N.305, E:Y.308, E:P.309, E:K.313 Salt bridges: E:K.137, E:K.313, E:K.313, E:K.317, E:K.317 GTP.21: 10 residues within 4Å: Chain F: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.187, F:T.300, F:D.301, F:D.301 GTP.22: 18 residues within 4Å: Chain F: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, A.298, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:E.186, F:Q.187, F:Q.187, F:L.269, F:N.273, F:N.273, F:N.305, F:Y.308, F:P.309, F:K.313 Salt bridges: F:K.137, F:K.313, F:K.313, F:K.317 GTP.25: 10 residues within 4Å: Chain G: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.187, G:T.300, G:D.301, G:D.301 GTP.26: 18 residues within 4Å: Chain G: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, A.298, D.301, L.302, N.305, Y.308, P.309, A.311, K.313, K.317 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:E.186, G:Q.187, G:Q.187, G:N.273, G:N.273, G:N.305, G:N.305, G:Y.308, G:K.313 Salt bridges: G:K.137, G:K.313, G:K.313, G:K.317, G:K.317 GTP.29: 10 residues within 4Å: Chain H: K.184, F.185, E.186, Q.187, I.190, P.193, A.298, T.300, D.301, K.304 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.187, H:T.300, H:D.301, H:D.301 GTP.30: 19 residues within 4Å: Chain H: K.137, E.186, Q.187, G.188, L.269, K.270, A.272, N.273, I.297, A.298, D.301, L.302, N.305, Y.308, P.309, L.310, A.311, K.313, K.317 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:E.186, H:Q.187, H:Q.187, H:N.273, H:N.305, H:P.309, H:P.309, H:A.311, H:K.313 Salt bridges: H:K.137, H:K.313, H:K.313, H:K.317

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 27 residues within 4Å: Chain A: S.143, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.143, A:N.378, A:R.397, A:S.404, A:S.404, A:D.439, A:D.439, A:G.441, A:G.462, A:S.463, A:Y.486, A:M.489, A:G.490, A:Q.516 IMP.7: 27 residues within 4Å: Chain B: S.143, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.143, B:N.378, B:R.397, B:S.404, B:S.404, B:D.439, B:D.439, B:G.441, B:G.462, B:S.463, B:Y.486, B:M.489, B:G.490, B:Q.516 IMP.11: 28 residues within 4Å: Chain C: S.143, P.144, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.143, C:N.378, C:R.397, C:S.404, C:S.404, C:D.439, C:D.439, C:G.441, C:G.462, C:S.463, C:Y.486, C:M.489, C:G.490, C:Q.516 IMP.15: 28 residues within 4Å: Chain D: S.143, P.144, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.397, D:S.404, D:S.404, D:S.404, D:D.439, D:D.439, D:G.441, D:I.442, D:G.462, D:S.463, D:Y.486, D:M.489, D:G.490, D:Q.516 IMP.19: 27 residues within 4Å: Chain E: S.143, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.143, E:N.378, E:R.397, E:S.404, E:S.404, E:D.439, E:D.439, E:G.441, E:G.462, E:S.463, E:Y.486, E:M.489, E:G.490, E:Q.516 IMP.23: 28 residues within 4Å: Chain F: S.143, P.144, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.143, F:N.378, F:R.397, F:S.404, F:S.404, F:D.439, F:D.439, F:G.441, F:G.462, F:S.463, F:Y.486, F:M.489, F:G.490, F:Q.516 IMP.27: 28 residues within 4Å: Chain G: S.143, P.144, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.28 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:S.143, G:R.397, G:S.404, G:S.404, G:D.439, G:D.439, G:G.441, G:G.462, G:S.463, G:Y.486, G:M.489, G:G.490, G:Q.516 IMP.31: 28 residues within 4Å: Chain H: S.143, P.144, M.145, N.378, R.397, G.403, S.404, I.405, C.406, I.407, T.408, D.439, G.440, G.441, I.442, M.460, M.461, G.462, S.463, L.464, Y.486, G.488, M.489, G.490, S.491, Q.516, G.517 Ligands: NAD.32 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:S.143, H:N.378, H:R.397, H:S.404, H:S.404, H:D.439, H:D.439, H:G.441, H:G.462, H:S.463, H:Y.486, H:M.489, H:G.490, H:Q.516

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

NAD.4: 23 residues within 4Å: Chain A: H.168, T.327, R.328, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Chain B: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.3 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:Q.544, B:Q.544, A:T.327, A:T.327, A:R.328, A:D.349, A:D.349, A:S.351, A:R.397, A:G.399, A:G.401 Hydrophobic interactions: A:Q.516 pi-Stacking: A:Y.357 pi-Cation interactions: A:R.328, A:R.328 NAD.8: 23 residues within 4Å: Chain B: H.168, T.327, R.328, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Chain C: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.7 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.516 Hydrogen bonds: B:T.327, B:T.327, B:R.328, B:D.349, B:D.349, B:S.351, B:S.351, B:R.397, B:G.399, B:G.401, C:Q.544, C:Q.544 pi-Stacking: B:Y.357 pi-Cation interactions: B:R.328, B:R.328 NAD.12: 23 residues within 4Å: Chain C: H.168, T.327, R.328, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Chain D: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.11 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Q.516 Hydrogen bonds: C:T.327, C:T.327, C:D.349, C:D.349, C:S.351, C:R.397, C:G.399, C:G.401, D:Q.544, D:Q.544 Salt bridges: C:R.328 pi-Stacking: C:Y.357 pi-Cation interactions: C:R.328 NAD.16: 23 residues within 4Å: Chain A: I.117, I.120, A.121, H.541, Q.544 Chain D: H.168, T.327, R.328, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Ligands: IMP.15 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.327, D:T.327, D:R.328, D:R.328, D:D.349, D:D.349, D:S.351, D:N.378, D:G.399, D:G.401, A:Q.544, A:Q.544 pi-Stacking: D:Y.357 pi-Cation interactions: D:R.328, D:R.328 NAD.20: 24 residues within 4Å: Chain E: H.168, T.327, R.328, E.329, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Chain F: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.19 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Q.516 Hydrogen bonds: E:T.327, E:T.327, E:R.328, E:D.349, E:D.349, E:S.351, E:S.351, E:R.397, E:G.399, E:G.401, F:Q.544, F:Q.544 pi-Stacking: E:Y.357 pi-Cation interactions: E:R.328, E:R.328 NAD.24: 25 residues within 4Å: Chain F: H.168, T.327, R.328, E.329, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, C.406, T.408, M.489, G.490, Q.516 Chain G: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.23 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:Q.516 Hydrogen bonds: F:T.327, F:T.327, F:R.328, F:D.349, F:D.349, F:S.351, F:S.351, F:R.397, F:G.399, F:G.401, G:Q.544, G:Q.544 pi-Stacking: F:Y.357 pi-Cation interactions: F:R.328, F:R.328 NAD.28: 24 residues within 4Å: Chain G: H.168, T.327, R.328, E.329, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, T.408, M.489, G.490, Q.516 Chain H: I.117, I.120, A.121, H.541, Q.544 Ligands: IMP.27 15 PLIP interactions: 13 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:T.327, G:T.327, G:R.328, G:D.349, G:D.349, G:S.351, G:S.351, G:N.378, G:G.399, G:G.401, H:Q.544, H:Q.544 pi-Stacking: G:Y.357 pi-Cation interactions: G:R.328, G:R.328 NAD.32: 25 residues within 4Å: Chain E: I.117, I.120, A.121, H.541, Q.544 Chain H: H.168, T.327, R.328, E.329, D.349, S.350, S.351, Q.352, Y.357, N.378, R.397, G.399, M.400, G.401, C.406, T.408, M.489, G.490, Q.516 Ligands: IMP.31 15 PLIP interactions: 2 interactions with chain E, 13 interactions with chain H Hydrogen bonds: E:Q.544, E:Q.544, H:T.327, H:T.327, H:R.328, H:D.349, H:D.349, H:S.351, H:R.397, H:G.399, H:G.401 Hydrophobic interactions: H:Q.516 pi-Stacking: H:Y.357 pi-Cation interactions: H:R.328, H:R.328

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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