SMTL ID : 7rgm.1

HUMAN RETINAL VARIANT IMPDH1(546) TREATED WITH ATP, IMP, 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: 19 residues within 4Å: Chain A: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain H: R.161, K.205 Ligands: ATP.2, ATP.29 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain H Hydrogen bonds: A:T.159, A:R.161, A:D.162, A:D.162, A:T.180, A:V.186, A:G.207, A:K.208, A:K.208, H:K.205 Salt bridges: A:R.161, A:R.161, H:R.161, H:R.161, H:R.161 ATP.2: 18 residues within 4Å: Chain A: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, I.221, A.223, T.225, D.226 Ligands: ATP.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.119, A:V.119, A:S.140, A:G.141, A:S.160, A:K.208, A:T.225, A:D.226, A:D.226 Salt bridges: A:K.134, A:K.208, A:K.208 pi-Stacking: A:F.139, A:F.139 ATP.5: 19 residues within 4Å: Chain B: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain G: R.161, K.205 Ligands: ATP.6, ATP.25 17 PLIP interactions: 2 interactions with chain G, 15 interactions with chain B Hydrogen bonds: G:K.205, B:T.159, B:S.160, B:S.160, B:S.160, B:R.161, B:D.162, B:D.162, B:T.180, B:V.186, B:V.186, B:K.206, B:G.207, B:K.208 Salt bridges: G:R.161, B:R.161, B:R.161 ATP.6: 18 residues within 4Å: Chain B: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, I.221, A.223, T.225, D.226 Ligands: ATP.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:V.119, B:V.119, B:S.140, B:S.140, B:G.141, B:S.160, B:K.208, B:T.225, B:D.226, B:D.226 Salt bridges: B:K.134, B:K.208, B:K.208 pi-Stacking: B:F.139, B:F.139 ATP.9: 19 residues within 4Å: Chain C: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain F: R.161, K.205 Ligands: ATP.10, ATP.21 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:T.159, C:S.160, C:S.160, C:R.161, C:D.162, C:D.162, C:T.180, C:V.186, C:G.207, C:K.208, C:K.208, F:K.205 Salt bridges: C:R.161, C:R.161, F:R.161, F:R.161, F:R.161 ATP.10: 18 residues within 4Å: Chain C: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, I.221, A.223, T.225, D.226 Ligands: ATP.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.119, C:V.119, C:S.140, C:G.141, C:S.160, C:K.208, C:T.225, C:D.226, C:D.226 Salt bridges: C:K.134, C:K.208, C:K.208 pi-Stacking: C:F.139, C:F.139 ATP.13: 18 residues within 4Å: Chain D: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Chain E: R.161, K.205 Ligands: ATP.17 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:T.159, D:T.159, D:R.161, D:D.162, D:D.162, D:V.186, D:K.206, D:G.207, D:K.208, D:K.208, E:K.205 Salt bridges: D:R.161, D:R.161, E:R.161, E:R.161 ATP.14: 17 residues within 4Å: Chain D: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, T.159, S.160, K.208, A.223, T.225, D.226 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:V.119, D:V.119, D:S.140, D:S.140, D:G.141, D:S.160, D:T.225, D:D.226, D:D.226 Salt bridges: D:K.134, D:K.208, D:K.208 pi-Stacking: D:F.139, D:F.139 ATP.17: 19 residues within 4Å: Chain D: R.161, K.205 Chain E: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: ATP.13, ATP.18 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:T.159, E:S.160, E:S.160, E:R.161, E:D.162, E:D.162, E:T.180, E:V.186, E:G.207, E:K.208, E:K.208, D:R.161, D:K.205 Salt bridges: E:R.161, D:R.161 ATP.18: 17 residues within 4Å: Chain E: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.17 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:V.119, E:V.119, E:S.140, E:G.141, E:S.160, E:K.208, E:T.225, E:D.226, E:D.226, E:D.226 Salt bridges: E:K.134, E:K.208, E:K.208 pi-Stacking: E:F.139, E:F.139 ATP.21: 19 residues within 4Å: Chain C: R.161, K.205 Chain F: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: ATP.9, ATP.22 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain F Hydrogen bonds: C:K.205, F:T.159, F:S.160, F:S.160, F:R.161, F:D.162, F:D.162, F:V.186, F:K.206, F:G.207, F:K.208, F:K.208 Salt bridges: C:R.161, C:R.161, F:R.161, F:R.161 ATP.22: 18 residues within 4Å: Chain F: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, I.221, A.223, T.225, D.226 Ligands: ATP.21 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:V.119, F:V.119, F:S.140, F:G.141, F:K.208, F:T.225, F:D.226, F:D.226 Salt bridges: F:K.134, F:K.208, F:K.208 pi-Stacking: F:F.139 ATP.25: 19 residues within 4Å: Chain B: R.161, K.205 Chain G: I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: ATP.5, ATP.26 17 PLIP interactions: 13 interactions with chain G, 4 interactions with chain B Hydrogen bonds: G:T.159, G:S.160, G:S.160, G:R.161, G:D.162, G:D.162, G:V.186, G:K.206, G:G.207, G:K.208, G:K.208, B:K.205 Salt bridges: G:R.161, G:R.161, B:R.161, B:R.161, B:R.161 ATP.26: 17 residues within 4Å: Chain G: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, A.223, T.225, D.226 Ligands: ATP.25 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.119, G:V.119, G:S.140, G:G.141, G:S.160, G:K.208, G:T.225, G:D.226, G:D.226 Salt bridges: G:K.134, G:K.208, G:K.208 pi-Stacking: G:F.139, G:F.139 ATP.29: 20 residues within 4Å: Chain A: R.161, K.205 Chain H: S.140, I.157, V.158, T.159, S.160, R.161, D.162, T.180, E.184, L.185, V.186, K.206, G.207, K.208, L.209, P.210 Ligands: ATP.1, ATP.30 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:T.159, H:S.160, H:S.160, H:R.161, H:D.162, H:D.162, H:T.180, H:V.186, H:V.186, H:K.206, H:G.207, H:K.208, A:K.205 Salt bridges: H:R.161, H:R.161, A:R.161, A:R.161 ATP.30: 18 residues within 4Å: Chain H: I.115, D.117, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, P.143, S.160, K.208, I.221, A.223, T.225, D.226 Ligands: ATP.29 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:V.119, H:V.119, H:S.140, H:S.140, H:G.141, H:S.160, H:K.208, H:T.225, H:D.226, 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: 29 residues within 4Å: Chain A: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442, V.443 Ligands: NAD.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.68, A:N.303, A:R.322, A:S.329, A:S.329, A:S.329, A:D.364, A:D.364, A:G.366, A:G.387, A:S.388, A:Y.411, A:M.414, A:G.415, A:Q.441 IMP.7: 26 residues within 4Å: Chain B: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, M.385, M.386, G.387, S.388, L.389, 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:N.303, B:R.322, B:S.329, B:S.329, B:S.329, B:D.364, B:D.364, B:G.366, B:G.387, B:S.388, B:Y.411, B:M.414, B:G.415, B:Q.441 IMP.11: 27 residues within 4Å: Chain C: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.68, C:N.303, C:R.322, C:S.329, C:D.364, C:D.364, C:G.366, C:G.387, C:S.388, C:Y.411, C:M.414, C:G.415, C:Q.441 IMP.15: 27 residues within 4Å: Chain D: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.68, D:N.303, D:R.322, D:S.329, D:D.364, D:D.364, D:G.366, D:G.387, D:S.388, D:Y.411, D:M.414, D:G.415, D:Q.441 IMP.19: 27 residues within 4Å: Chain E: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.20 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.68, E:N.303, E:R.322, E:S.329, E:D.364, E:D.364, E:G.366, E:G.387, E:S.388, E:Y.411, E:M.414, E:G.415, E:Q.441 IMP.23: 27 residues within 4Å: Chain F: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, T.333, D.364, G.365, G.366, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.24 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.68, F:N.303, F:R.322, F:S.329, F:D.364, F:D.364, F:G.366, F:G.387, F:S.388, F:Y.411, F:M.414, F:G.415, F:Q.441 IMP.27: 27 residues within 4Å: Chain F: H.504 Chain G: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, I.332, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, Q.441, G.442 Ligands: NAD.28 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.68, G:R.322, G:R.322, G:S.329, G:S.329, G:S.329, G:D.364, G:D.364, G:G.366, G:G.387, G:S.388, G:Y.411, G:M.414, G:G.415 IMP.31: 27 residues within 4Å: Chain H: S.68, P.69, M.70, N.303, R.322, G.328, S.329, I.330, C.331, T.333, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, L.389, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: NAD.32 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.68, H:N.303, H:R.322, H:S.329, H:S.329, H:S.329, H:D.364, H:D.364, H:G.366, H:G.387, H:S.388, H:Y.411, H:M.414, H:G.415, H:Q.441

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

NAD.4: 24 residues within 4Å: Chain A: H.93, T.252, R.253, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Chain D: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.3 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain A Hydrogen bonds: D:Q.469, D:Q.469, A:T.252, A:T.252, A:R.253, A:D.274, A:D.274, A:S.275, A:S.276, A:S.276, A:G.324, A:G.326 pi-Stacking: A:Y.282 pi-Cation interactions: A:R.253, A:R.253 NAD.8: 24 residues within 4Å: Chain A: I.42, I.45, A.46, H.466, Q.469 Chain B: H.93, T.252, R.253, D.274, S.275, S.276, Y.282, N.303, R.322, G.324, M.325, G.326, G.328, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.7 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.441 Hydrogen bonds: B:T.252, B:T.252, B:R.253, B:R.253, B:D.274, B:D.274, B:S.275, B:S.276, B:S.276, B:G.326, A:Q.469, A:Q.469 pi-Stacking: B:Y.282 pi-Cation interactions: B:R.253, B:R.253 NAD.12: 24 residues within 4Å: Chain B: I.42, I.45, A.46, H.466, Q.469 Chain C: H.93, T.252, R.253, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.11 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.441 Hydrogen bonds: C:T.252, C:T.252, C:R.253, C:D.274, C:D.274, C:S.275, C:S.276, C:S.276, C:G.326, B:Q.469, B:Q.469 pi-Stacking: C:Y.282 pi-Cation interactions: C:R.253, C:R.253 NAD.16: 23 residues within 4Å: Chain C: I.42, I.45, A.46, H.466, Q.469 Chain D: H.93, T.252, R.253, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, T.333, M.414, G.415, Q.441 Ligands: IMP.15 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.252, D:T.252, D:R.253, D:R.253, D:D.274, D:D.274, D:S.275, D:S.276, D:S.276, D:Y.282, D:G.324, D:G.326, C:Q.469, C:Q.469 pi-Stacking: D:Y.282 pi-Cation interactions: D:R.253, D:R.253 NAD.20: 25 residues within 4Å: Chain E: H.93, T.252, R.253, D.274, S.275, S.276, Q.277, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Chain H: I.42, I.45, A.46, H.466, Q.469 Ligands: IMP.19 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:T.252, E:T.252, E:R.253, E:R.253, E:D.274, E:D.274, E:S.275, E:S.276, E:S.276, E:G.324, E:G.326, H:Q.469, H:Q.469 pi-Stacking: E:Y.282 pi-Cation interactions: E:R.253, E:R.253 NAD.24: 27 residues within 4Å: Chain E: I.42, I.45, A.46, H.466, Q.469 Chain F: H.93, T.252, R.253, D.274, S.275, S.276, Q.277, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, C.327, G.328, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.23 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:T.252, F:T.252, F:R.253, F:R.253, F:D.274, F:D.274, F:S.275, F:S.276, F:S.276, F:Y.282, F:G.326, E:Q.469, E:Q.469 pi-Stacking: F:Y.282 pi-Cation interactions: F:R.253, F:R.253 NAD.28: 24 residues within 4Å: Chain F: I.42, I.45, A.46, H.466, Q.469 Chain G: H.93, T.252, R.253, D.274, S.275, S.276, Q.277, Y.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.27 18 PLIP interactions: 2 interactions with chain F, 16 interactions with chain G Hydrogen bonds: F:Q.469, F:Q.469, G:T.252, G:T.252, G:R.253, G:R.253, G:D.274, G:D.274, G:S.275, G:S.275, G:S.276, G:S.276, G:Y.282, G:G.324, G:G.326 pi-Stacking: G:Y.282 pi-Cation interactions: G:R.253, G:R.253 NAD.32: 26 residues within 4Å: Chain G: I.42, I.45, A.46, H.466, Q.469 Chain H: H.93, T.252, R.253, D.274, S.275, S.276, S.280, Y.282, N.303, R.322, G.324, M.325, G.326, C.327, G.328, C.331, T.333, M.414, G.415, Q.441 Ligands: IMP.31 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:T.252, H:T.252, H:R.253, H:R.253, H:D.274, H:D.274, H:S.275, H:S.276, H:S.276, H:G.326, G:Q.469, G:Q.469 pi-Stacking: H:Y.282 pi-Cation interactions: H:R.253, 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

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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