SMTL ID : 7rfe.1

HUMAN IMPDH1 TREATED WITH GTP, 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: 17 residues within 4Å: Chain A: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.102, A:Q.102, A:N.188, A:N.220, A:Y.223, A:P.224, A:K.228 Salt bridges: A:K.52, A:K.52, A:K.228, A:K.228, A:K.232, A:K.232 GTP.2: 21 residues within 4Å: Chain A: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, I.132, T.149, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.102, A:V.109, A:S.130, A:S.130, A:G.131, A:G.131, A:G.131, A:T.215, A:D.216, A:D.216, A:K.219 Salt bridges: A:K.124, A:K.198, A:K.198 pi-Stacking: A:F.129, A:F.129 pi-Cation interactions: A:F.129 GTP.5: 18 residues within 4Å: Chain B: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, Q.192, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.102, B:G.103, B:N.188, B:N.220, B:Y.223, B:P.224, B:K.228 Salt bridges: B:K.52, B:K.52, B:K.228, B:K.228, B:K.232, B:K.232 GTP.6: 20 residues within 4Å: Chain B: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, I.132, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.7 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.99, B:Q.102, B:Q.102, B:V.109, B:S.130, B:G.131, B:G.131, B:G.131, B:S.150, B:K.198, B:T.215, B:D.216, B:D.216, B:K.219 Salt bridges: B:K.124, B:K.198, B:K.198 pi-Cation interactions: B:F.129 GTP.9: 17 residues within 4Å: Chain C: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.102, C:Q.102, C:N.188, C:N.220, C:Y.223, C:P.224, C:K.228 Salt bridges: C:K.52, C:K.52, C:K.228, C:K.228, C:K.232, C:K.232 GTP.10: 20 residues within 4Å: Chain C: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, T.149, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.11 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.99, C:Q.102, C:V.109, C:S.130, C:G.131, C:G.131, C:G.131, C:T.215, C:D.216, C:D.216, C:K.219 Salt bridges: C:K.124, C:K.124, C:K.198, C:K.198 pi-Stacking: C:F.129, C:F.129 pi-Cation interactions: C:F.129 GTP.13: 17 residues within 4Å: Chain D: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Q.102, D:Q.102, D:N.188, D:N.220, D:Y.223, D:P.224, D:K.228 Salt bridges: D:K.52, D:K.52, D:K.228, D:K.228, D:K.232, D:K.232 GTP.14: 19 residues within 4Å: Chain D: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.15 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:K.99, D:Q.102, D:V.109, D:S.130, D:G.131, D:G.131, D:G.131, D:K.198, D:T.215, D:D.216, D:D.216, D:K.219 Salt bridges: D:K.124, D:K.198, D:K.198 pi-Stacking: D:F.129 pi-Cation interactions: D:F.129 GTP.17: 18 residues within 4Å: Chain E: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, Q.192, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:E.101, E:Q.102, E:Q.102, E:N.188, E:N.220, E:Y.223, E:P.224, E:K.228 Salt bridges: E:K.52, E:K.52, E:K.228, E:K.228, E:K.232, E:K.232 GTP.18: 20 residues within 4Å: Chain E: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, T.149, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.19 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:K.99, E:Q.102, E:V.109, E:S.130, E:G.131, E:G.131, E:G.131, E:T.215, E:D.216, E:D.216, E:K.219 Salt bridges: E:K.124, E:K.124, E:K.198, E:K.198 pi-Stacking: E:F.129, E:F.129 pi-Cation interactions: E:F.129 GTP.21: 16 residues within 4Å: Chain F: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, Q.192, I.212, A.213, D.216, L.217, N.220, P.224, K.228, K.232 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:E.101, F:Q.102, F:G.103, F:N.188, F:N.188, F:N.188, F:N.220, F:N.220, F:P.224, F:K.228 Salt bridges: F:K.52, F:K.52, F:K.228, F:K.228, F:K.232, F:K.232 GTP.22: 18 residues within 4Å: Chain F: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, F.129, S.130, G.131, T.149, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.23 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:Q.102, F:Q.102, F:V.109, F:S.130, F:S.130, F:S.130, F:G.131, F:G.131, F:G.131, F:S.150, F:T.215, F:D.216, F:D.216, F:K.219 Salt bridges: F:K.198, F:K.198 pi-Stacking: F:F.129, F:F.129 pi-Cation interactions: F:F.129 GTP.25: 17 residues within 4Å: Chain G: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:E.101, G:Q.102, G:Q.102, G:N.188, G:N.188, G:N.220, G:Y.223, G:P.224, G:K.228 Salt bridges: G:K.52, G:K.52, G:K.228, G:K.228, G:K.232, G:K.232 GTP.26: 21 residues within 4Å: Chain G: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, I.132, T.149, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.27 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:K.99, G:Q.102, G:V.109, G:S.130, G:S.130, G:G.131, G:G.131, G:G.131, G:S.150, G:T.215, G:D.216, G:D.216, G:K.219 Salt bridges: G:K.124, G:K.198, G:K.198 pi-Stacking: G:F.129, G:F.129 pi-Cation interactions: G:F.129 GTP.29: 17 residues within 4Å: Chain H: K.52, E.101, Q.102, G.103, L.184, K.185, N.188, I.212, A.213, D.216, L.217, N.220, Y.223, P.224, A.226, K.228, K.232 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:E.101, H:Q.102, H:Q.102, H:N.188, H:N.220, H:Y.223, H:P.224, H:K.228 Salt bridges: H:K.52, H:K.52, H:K.228, H:K.228, H:K.232, H:K.232 GTP.30: 20 residues within 4Å: Chain H: K.99, F.100, E.101, Q.102, I.105, P.108, V.109, K.124, G.128, F.129, S.130, G.131, I.132, S.150, K.198, A.213, T.215, D.216, K.219 Ligands: ATP.31 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:K.99, H:Q.102, H:Q.102, H:V.109, H:S.130, H:S.130, H:G.131, H:G.131, H:G.131, H:S.150, H:K.198, H:T.215, H:D.216, H:D.216, H:K.219 Salt bridges: H:K.124, H:K.198, H:K.198 pi-Stacking: H:F.129 pi-Cation interactions: H:F.129

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

ATP.3: 16 residues within 4Å: Chain A: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.149, A:S.150, A:S.150, A:R.151, A:R.151, A:D.152, A:D.152, A:T.170, A:V.176, A:G.197, A:K.198, A:K.198 Salt bridges: A:R.151, A:K.198, A:K.198 ATP.7: 16 residues within 4Å: Chain B: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.149, B:S.150, B:R.151, B:D.152, B:D.152, B:T.170, B:V.176, B:G.197, B:K.198, B:K.198 Salt bridges: B:R.151, B:R.151 ATP.11: 16 residues within 4Å: Chain C: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.149, C:S.150, C:S.150, C:R.151, C:D.152, C:D.152, C:T.170, C:V.176, C:G.197, C:K.198, C:K.198 Salt bridges: C:R.151, C:K.198, C:K.198 ATP.15: 16 residues within 4Å: Chain D: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.14 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.149, D:S.150, D:S.150, D:S.150, D:R.151, D:D.152, D:D.152, D:T.170, D:V.176, D:G.197, D:K.198, D:K.198 Salt bridges: D:R.151, D:R.151 ATP.19: 16 residues within 4Å: Chain E: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.18 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:T.149, E:S.150, E:S.150, E:R.151, E:D.152, E:D.152, E:T.170, E:T.170, E:V.176, E:G.197, E:K.198, E:K.198 Salt bridges: E:R.151, E:K.198, E:K.198 ATP.23: 16 residues within 4Å: Chain F: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.22 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:T.149, F:R.151, F:D.152, F:D.152, F:T.170, F:V.176, F:G.197, F:K.198, F:K.198 Salt bridges: F:R.151, F:R.151, F:K.198, F:K.198 ATP.27: 16 residues within 4Å: Chain G: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.26 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:T.149, G:S.150, G:R.151, G:D.152, G:D.152, G:T.170, G:V.176, G:G.197, G:K.198, G:K.198 Salt bridges: G:R.151, G:R.151, G:K.198, G:K.198 ATP.31: 16 residues within 4Å: Chain H: I.147, V.148, T.149, S.150, R.151, D.152, T.170, E.174, L.175, V.176, K.196, G.197, K.198, L.199, P.200 Ligands: GTP.30 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:T.149, H:R.151, H:D.152, H:D.152, H:T.170, H:V.176, H:G.197, H:K.198, H:K.198 Salt bridges: H:R.151, H:R.151

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 28 residues within 4Å: Chain A: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.58, A:N.293, A:R.312, A:S.319, A:D.354, A:D.354, A:G.356, A:G.377, A:S.378, A:S.378, A:S.378, A:S.378, A:Y.401, A:M.404, A:G.405, A:Q.431 IMP.8: 28 residues within 4Å: Chain B: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.58, B:N.293, B:R.312, B:S.319, B:D.354, B:D.354, B:G.356, B:G.377, B:S.378, B:S.378, B:S.378, B:S.378, B:Y.401, B:M.404, B:G.405, B:Q.431 IMP.12: 29 residues within 4Å: Chain C: S.58, P.59, M.60, S.266, N.293, R.312, C.317, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.58, C:N.293, C:R.312, C:S.319, C:D.354, C:D.354, C:G.356, C:G.377, C:S.378, C:S.378, C:S.378, C:S.378, C:Y.401, C:M.404, C:G.405, C:Q.431 IMP.16: 28 residues within 4Å: Chain D: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.58, D:N.293, D:R.312, D:S.319, D:D.354, D:D.354, D:G.356, D:G.377, D:S.378, D:S.378, D:S.378, D:S.378, D:Y.401, D:M.404, D:G.405, D:Q.431 IMP.20: 28 residues within 4Å: Chain E: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.58, E:N.293, E:R.312, E:S.319, E:D.354, E:D.354, E:G.356, E:G.377, E:S.378, E:S.378, E:S.378, E:S.378, E:Y.401, E:M.404, E:G.405, E:Q.431 IMP.24: 28 residues within 4Å: Chain F: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.58, F:N.293, F:R.312, F:S.319, F:D.354, F:D.354, F:G.356, F:G.377, F:S.378, F:S.378, F:S.378, F:S.378, F:Y.401, F:M.404, F:G.405, F:Q.431 IMP.28: 28 residues within 4Å: Chain G: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:S.58, G:N.293, G:R.312, G:S.319, G:D.354, G:D.354, G:G.356, G:G.377, G:S.378, G:S.378, G:S.378, G:S.378, G:Y.401, G:M.404, G:G.405, G:Q.431 IMP.32: 28 residues within 4Å: Chain H: S.58, P.59, M.60, S.266, N.293, R.312, G.318, S.319, I.320, C.321, I.322, T.323, D.354, G.355, G.356, I.357, M.375, M.376, G.377, S.378, L.379, Y.401, G.403, M.404, G.405, S.406, Q.431, G.432 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:S.58, H:N.293, H:R.312, H:S.319, H:D.354, H:D.354, H:G.356, H:G.377, H:S.378, H:S.378, H:S.378, H:S.378, H:Y.401, H:M.404, H:G.405, H:Q.431

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