SMTL ID : 7rfg.1

HUMAN IMPDH1 TREATED WITH GTP, IMP, AND NAD+ OCTAMER-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.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.112, A:G.113, A:N.198, A:N.198, A:N.230, A:Y.233, A:P.234, A:K.238 Salt bridges: A:K.62, A:K.62, A:K.238, A:K.238, A:K.242, A:K.242 GTP.2: 19 residues within 4Å: Chain A: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.109, A:Q.112, A:V.119, A:S.140, A:G.141, A:G.141, A:G.141, A:S.160, A:K.208, A:T.225, A:D.226, A:D.226, A:K.229 Salt bridges: A:K.134, A:K.208, A:K.208 pi-Stacking: A:F.139 pi-Cation interactions: A:F.139 GTP.5: 17 residues within 4Å: Chain B: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.112, B:G.113, B:N.198, B:N.198, B:N.230, B:Y.233, B:P.234, B:K.238 Salt bridges: B:K.62, B:K.62, B:K.238, B:K.238, B:K.242, B:K.242 GTP.6: 18 residues within 4Å: Chain B: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.109, B:Q.112, B:V.119, B:S.140, B:S.140, B:G.141, B:G.141, B:G.141, B:S.160, B:K.208, B:T.225, B:D.226, B:D.226, B:K.229 Salt bridges: B:K.134, B:K.208, B:K.208 pi-Stacking: B:F.139 pi-Cation interactions: B:F.139 GTP.9: 17 residues within 4Å: Chain C: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.112, C:N.198, C:N.198, C:N.198, C:N.230, C:Y.233, C:P.234, C:K.238 Salt bridges: C:K.62, C:K.62, C:K.238, C:K.238, C:K.242, C:K.242 GTP.10: 20 residues within 4Å: Chain C: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, I.142, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.11 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:K.109, C:Q.112, C:V.119, C:S.140, C:G.141, C:G.141, C:G.141, C:S.160, C:T.225, C:D.226, C:D.226, C:K.229 Salt bridges: C:K.134, C:K.208, C:K.208 pi-Stacking: C:F.139 pi-Cation interactions: C:F.139 GTP.13: 17 residues within 4Å: Chain D: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.112, D:Q.112, D:N.198, D:N.198, D:N.230, D:Y.233, D:P.234, D:K.238 Salt bridges: D:K.62, D:K.62, D:K.238, D:K.238, D:K.242, D:K.242 GTP.14: 19 residues within 4Å: Chain D: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.15 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:K.109, D:Q.112, D:V.119, D:S.140, D:S.140, D:G.141, D:G.141, D:G.141, D:S.160, D:K.208, D:T.225, D:D.226, D:D.226, D:K.229 Salt bridges: D:K.134, D:K.208, D:K.208 pi-Stacking: D:F.139, D:F.139 pi-Cation interactions: D:F.139 GTP.17: 17 residues within 4Å: Chain E: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:E.111, E:Q.112, E:Q.112, E:N.198, E:N.198, E:N.230, E:Y.233, E:P.234, E:K.238 Salt bridges: E:K.62, E:K.62, E:K.238, E:K.238, E:K.242, E:K.242 GTP.18: 19 residues within 4Å: Chain E: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.19 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:K.109, E:Q.112, E:V.119, E:S.140, E:S.140, E:G.141, E:G.141, E:G.141, E:S.160, E:K.208, E:T.225, E:D.226, E:D.226, E:K.229 Salt bridges: E:K.134, E:K.208, E:K.208 pi-Stacking: E:F.139 pi-Cation interactions: E:F.139 GTP.21: 17 residues within 4Å: Chain F: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:E.111, F:Q.112, F:N.198, F:N.198, F:N.198, F:N.230, F:Y.233, F:P.234, F:K.238 Salt bridges: F:K.62, F:K.62, F:K.238, F:K.238, F:K.242, F:K.242 GTP.22: 18 residues within 4Å: Chain F: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.23 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.109, F:Q.112, F:V.119, F:S.140, F:G.141, F:G.141, F:G.141, F:T.225, F:D.226, F:D.226, F:K.229 Salt bridges: F:K.134, F:K.208, F:K.208 pi-Stacking: F:F.139, F:F.139 pi-Cation interactions: F:F.139 GTP.25: 17 residues within 4Å: Chain G: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:E.111, G:Q.112, G:Q.112, G:N.198, G:N.198, G:N.230, G:N.230, G:Y.233, G:K.238 Salt bridges: G:K.62, G:K.62, G:K.238, G:K.238, G:K.242, G:K.242 GTP.26: 19 residues within 4Å: Chain G: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, G.138, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.27 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:K.109, G:Q.112, G:V.119, G:S.140, G:S.140, G:G.141, G:G.141, G:G.141, G:S.160, G:K.208, G:T.225, G:D.226, G:D.226, G:K.229 Salt bridges: G:K.134, G:K.208, G:K.208 pi-Cation interactions: G:F.139 GTP.29: 17 residues within 4Å: Chain H: K.62, E.111, Q.112, G.113, L.194, K.195, N.198, I.222, A.223, D.226, L.227, N.230, Y.233, P.234, A.236, K.238, K.242 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:E.111, H:Q.112, H:Q.112, H:N.198, H:N.198, H:N.230, H:Y.233, H:P.234, H:K.238 Salt bridges: H:K.62, H:K.62, H:K.238, H:K.238, H:K.242, H:K.242 GTP.30: 18 residues within 4Å: Chain H: K.109, F.110, E.111, Q.112, I.115, P.118, V.119, K.134, F.139, S.140, G.141, S.160, K.208, A.223, T.225, D.226, K.229 Ligands: ATP.31 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:K.109, H:Q.112, H:V.119, H:S.140, H:S.140, H:G.141, H:G.141, H:G.141, H:S.160, H:K.208, H:T.225, H:D.226, H:D.226, H:K.229 Salt bridges: H:K.134, H:K.208, H:K.208 pi-Stacking: H:F.139, H:F.139 pi-Cation interactions: H:F.139

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

ATP.3: 20 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 G: R.161, K.205, R.224, K.228 Ligands: GTP.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain G Hydrogen bonds: A:T.159, A:S.160, A:R.161, A:D.162, A:D.162, A:T.180, A:V.186, A:G.207, A:K.208, A:K.208 Salt bridges: A:R.161, A:R.161, G:R.161, G:R.161 ATP.7: 20 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 F: R.161, K.205, R.224 Ligands: GTP.6, ATP.23 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:T.159, B:R.161, B:D.162, B:D.162, B:T.180, B:V.186, B:G.207, B:K.208, B:K.208 Salt bridges: B:R.161, B:R.161, F:R.161, F:R.161 ATP.11: 18 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 E: R.161, K.205 Ligands: GTP.10 15 PLIP interactions: 2 interactions with chain E, 13 interactions with chain C Salt bridges: E:R.161, E:R.161, C:R.161, C:R.161, C:K.208, C:K.208 Hydrogen bonds: C:T.159, C:R.161, C:D.162, C:D.162, C:T.180, C:V.186, C:G.207, C:K.208, C:K.208 ATP.15: 19 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 H: R.161, K.205, K.228 Ligands: GTP.14 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain H Hydrogen bonds: D:T.159, D:S.160, D:S.160, D:R.161, D:D.162, D:D.162, D:T.180, D:V.186, D:G.207, D:K.208, D:K.208, H:R.161 Salt bridges: D:R.161, D:R.161, H:R.161 ATP.19: 20 residues within 4Å: Chain C: R.161, K.205, R.224, K.228 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: GTP.18 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain E Salt bridges: C:R.161, C:R.161, C:K.228, E:R.161, E:R.161 Hydrogen bonds: E:T.159, E:R.161, E:D.162, E:D.162, E:T.180, E:V.186, E:G.207, E:K.208, E:K.208 ATP.23: 19 residues within 4Å: Chain B: 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.7, GTP.22 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain F Hydrogen bonds: B:R.161, F:T.159, F:S.160, F:S.160, F:S.160, F:R.161, F:D.162, F:D.162, F:T.180, F:V.186, F:G.207, F:K.208, F:K.208 Salt bridges: B:R.161, F:R.161, F:R.161, F:K.208, F:K.208 ATP.27: 19 residues within 4Å: Chain A: R.161, K.205, R.224 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: GTP.26 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:T.159, G:R.161, G:D.162, G:D.162, G:T.180, G:V.186, G:G.207, G:K.208, G:K.208 Salt bridges: G:R.161, G:R.161, A:R.161, A:R.161 ATP.31: 19 residues within 4Å: Chain D: R.161, K.205, R.224 Chain H: 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: GTP.30 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:T.159, H:R.161, H:D.162, H:D.162, H:T.180, H:V.186, H:G.207, H:K.208, H:K.208 Salt bridges: H:R.161, H:R.161, D:R.161, D:R.161

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 27 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.68, A:N.303, A:R.322, A:S.329, A:S.329, A:D.364, A:D.364, A:G.366, A:G.387, A:S.388, A:S.388, A:S.388, A:S.388, A:Y.411, A:M.414, A:G.415, A:Q.441 IMP.8: 27 residues within 4Å: Chain B: 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 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.68, B:N.303, B:R.322, B:S.329, B:S.329, B:D.364, B:D.364, B:G.366, B:G.387, B:S.388, B:S.388, B:S.388, B:S.388, B:Y.411, B:M.414, B:G.415, B:Q.441 IMP.12: 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, 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 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.68, C:N.303, C:R.322, C:S.329, C:S.329, C:D.364, C:D.364, C:G.366, C:G.387, C:S.388, C:S.388, C:S.388, C:S.388, C:Y.411, C:M.414, C:G.415, C:Q.441 IMP.16: 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, 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 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.68, D:N.303, D:R.322, D:S.329, D:S.329, D:D.364, D:D.364, D:G.366, D:G.387, D:S.388, D:S.388, D:S.388, D:S.388, D:Y.411, D:M.414, D:G.415, D:Q.441 IMP.20: 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, 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 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.68, E:R.322, E:S.329, E:S.329, E:D.364, E:D.364, E:G.366, E:G.387, E:S.388, E:S.388, E:S.388, E:S.388, E:Y.411, E:M.414, E:G.415, E:Q.441 IMP.24: 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, 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 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:S.68, F:N.303, F:R.322, F:S.329, F:S.329, F:D.364, F:D.364, F:G.366, F:G.387, F:S.388, F:S.388, F:S.388, F:S.388, F:Y.411, F:M.414, F:G.415, F:Q.441 IMP.28: 27 residues within 4Å: Chain G: 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 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:S.68, G:N.303, G:R.322, G:S.329, G:S.329, G:D.364, G:D.364, G:G.366, G:G.387, G:S.388, G:S.388, G:S.388, G:S.388, G:Y.411, G:M.414, G:G.415, G:Q.441 IMP.32: 27 residues within 4Å: Chain H: 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 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:S.68, H:N.303, H:R.322, H:S.329, H:S.329, H:D.364, H:D.364, H:G.366, H:G.387, H:S.388, H:S.388, H:S.388, H:S.388, H:Y.411, H:M.414, H:G.415, H:Q.441

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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