SMTL ID : 8g9b.1

Human IMPDH2 mutant - L245P, treated with GTP, ATP, IMP, and NAD+; compressed filament segment reconstruction

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.114, Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.124, A:C.145, A:G.146, A:G.146, A:G.146, A:T.230, A:T.230, A:D.231 Salt bridges: A:K.213, A:K.213 pi-Stacking: A:F.144 pi-Cation interactions: A:F.144 GTP.2: 9 residues within 4Å: Chain A: E.116, G.118, L.199, N.203, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.116, A:E.116, A:N.203, A:N.203 Salt bridges: A:D.231, A:K.247 GTP.6: 15 residues within 4Å: Chain B: K.114, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:V.124, B:G.143, B:C.145, B:G.146, B:G.146, B:S.165, B:K.213, B:T.230, B:D.231 Salt bridges: B:K.213, B:K.213 pi-Stacking: B:F.144 pi-Cation interactions: B:F.144 GTP.7: 9 residues within 4Å: Chain B: E.116, G.118, F.119, L.199, N.203, D.231, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.116, B:E.116, B:F.119, B:N.203, B:N.203, B:K.243 Salt bridges: B:D.231, B:K.247 GTP.11: 15 residues within 4Å: Chain C: K.114, Y.115, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.13 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.124, C:C.145, C:G.146, C:G.146, C:G.146, C:S.165, C:S.165, C:T.230, C:T.230, C:D.231 Salt bridges: C:K.213, C:K.213 pi-Stacking: C:F.144 pi-Cation interactions: C:F.144 GTP.12: 10 residues within 4Å: Chain C: E.116, G.118, L.199, N.203, I.227, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.118, C:N.203, C:N.203, C:N.235 Salt bridges: C:D.231, C:K.247 GTP.16: 14 residues within 4Å: Chain D: K.114, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.18 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:V.124, D:C.145, D:G.146, D:G.146, D:K.213, D:T.230, D:T.230, D:D.231 Salt bridges: D:K.213, D:K.213 pi-Stacking: D:F.144, D:F.144 pi-Cation interactions: D:F.144 GTP.17: 9 residues within 4Å: Chain D: E.116, G.118, L.199, N.203, D.231, L.232, N.235, K.243, K.247 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.116, D:E.116, D:N.203 Salt bridges: D:D.231, D:K.247 GTP.21: 15 residues within 4Å: Chain E: K.114, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.23 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:V.124, E:C.145, E:G.146, E:G.146, E:S.165, E:T.230, E:T.230, E:D.231 Salt bridges: E:K.213, E:K.213 pi-Stacking: E:F.144, E:F.144 pi-Cation interactions: E:F.144 GTP.22: 9 residues within 4Å: Chain E: E.116, G.118, L.199, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:E.116, E:G.118, E:N.203, E:N.203, E:N.235 Salt bridges: E:D.231, E:K.247 GTP.26: 18 residues within 4Å: Chain F: K.114, Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.28 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Q.117, F:V.124, F:C.145, F:G.146, F:G.146, F:S.164, F:T.230, F:T.230, F:D.231 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.144 pi-Cation interactions: F:F.144 GTP.27: 9 residues within 4Å: Chain F: E.116, G.118, L.199, N.203, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.116, F:F.119, F:N.203, F:N.203 Salt bridges: F:D.231, F:K.247 GTP.31: 15 residues within 4Å: Chain G: K.114, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231, K.234 Ligands: ATP.33 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:V.124, G:C.145, G:G.146, G:G.146, G:T.230, G:T.230, G:D.231 pi-Stacking: G:F.144, G:F.144 pi-Cation interactions: G:F.144 GTP.32: 10 residues within 4Å: Chain G: E.116, G.118, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.116, G:G.118, G:N.203, G:N.203, G:N.235, G:K.243 Salt bridges: G:D.231, G:K.247, G:K.247 GTP.36: 13 residues within 4Å: Chain H: K.114, Q.117, I.120, P.123, V.124, G.143, F.144, C.145, G.146, K.213, A.228, T.230, D.231 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:V.124, H:G.143, H:C.145, H:G.146, H:G.146, H:T.230, H:T.230, H:D.231 Salt bridges: H:K.213, H:K.213 pi-Stacking: H:F.144 pi-Cation interactions: H:F.144 GTP.37: 11 residues within 4Å: Chain H: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:G.118, H:N.203, H:N.203 Salt bridges: H:D.231, H:K.247

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

ATP.3: 13 residues within 4Å: Chain A: S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Chain F: R.166 Ligands: GTP.1, ATP.28 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:S.164, A:S.165, A:R.166, A:D.167, A:T.185, A:V.191, A:V.191, F:R.166 Salt bridges: A:R.166, A:R.166, F:R.166 ATP.8: 13 residues within 4Å: Chain B: S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Chain E: R.166 Ligands: GTP.6, ATP.23 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:S.164, B:S.165, B:R.166, B:D.167, B:D.167, B:T.185, B:V.191, B:V.191 Salt bridges: B:R.166, B:R.166, B:R.166, E:R.166, E:R.166 ATP.13: 13 residues within 4Å: Chain C: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Chain H: R.166 Ligands: GTP.11 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:S.164, C:S.164, C:S.165, C:R.166, C:D.167, C:D.167, C:T.185, C:V.191, C:V.191, C:K.211 Salt bridges: C:R.166, C:R.166, H:R.166 ATP.18: 13 residues within 4Å: Chain D: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Chain G: R.166 Ligands: GTP.16 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:S.164, D:R.166, D:D.167, D:D.167, D:D.169, D:T.185, D:V.191, D:V.191 Salt bridges: D:R.166, D:R.166, G:R.166, G:R.166, G:K.233 ATP.23: 12 residues within 4Å: Chain B: R.166 Chain E: S.164, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.8, GTP.21 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:S.164, E:R.166, E:D.167, E:D.167, E:T.185, E:V.191, E:V.191, E:K.211 Salt bridges: E:R.166, E:R.166, E:K.213, B:R.166, B:R.166, B:R.166 ATP.28: 14 residues within 4Å: Chain A: R.166 Chain F: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.3, GTP.26 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:S.164, F:S.164, F:S.164, F:S.165, F:D.167, F:T.185, F:V.191, F:V.191 Salt bridges: F:R.166, F:R.166, F:R.166, F:K.213, A:R.166, A:R.166 ATP.33: 14 residues within 4Å: Chain D: R.166, K.233 Chain G: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 Ligands: GTP.31 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain G Salt bridges: D:R.166, D:R.166, D:K.233, G:R.166, G:R.166 Hydrogen bonds: G:S.164, G:D.167, G:D.167, G:T.185, G:V.191, G:K.213 ATP.38: 14 residues within 4Å: Chain C: R.166, K.210, K.233 Chain H: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain C Hydrogen bonds: H:S.164, H:D.167, H:T.185, H:V.191, H:V.191 Salt bridges: H:R.166, H:R.166, H:R.166, H:K.213, C:R.166, C:R.166, C:K.233

8 x IMP: INOSINIC ACID(Covalent)

IMP.4: 21 residues within 4Å: Chain A: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.73, A:N.308, A:R.327, A:R.327, A:S.334, A:S.334, A:G.371, A:I.372, A:G.392, A:S.393, A:M.419, A:G.420, A:S.421, A:Q.446 IMP.9: 22 residues within 4Å: Chain B: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.308, B:R.327, B:R.327, B:S.334, B:G.371, B:I.372, B:G.392, B:S.393, B:M.419, B:G.420, B:S.421, B:Q.446 IMP.14: 22 residues within 4Å: Chain C: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, T.338, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.15 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.73, C:S.73, C:N.308, C:R.327, C:R.327, C:S.334, C:G.371, C:I.372, C:G.392, C:S.393, C:M.419, C:G.420, C:Q.446 IMP.19: 23 residues within 4Å: Chain D: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.20 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.73, D:N.308, D:R.327, D:R.327, D:S.334, D:G.370, D:G.371, D:G.392, D:S.393, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.24: 21 residues within 4Å: Chain E: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.25 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.73, E:N.308, E:R.327, E:R.327, E:S.334, E:G.371, E:G.392, E:S.393, E:Y.416, E:M.419, E:G.420, E:S.421, E:Q.446 IMP.29: 22 residues within 4Å: Chain F: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.30 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.73, F:N.308, F:R.327, F:R.327, F:S.334, F:D.369, F:G.371, F:G.392, F:S.393, F:Y.416, F:M.419, F:G.420, F:S.421, F:Q.446 IMP.34: 21 residues within 4Å: Chain G: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.35 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.73, G:N.308, G:R.327, G:R.327, G:S.334, G:D.369, G:G.370, G:G.371, G:G.392, G:S.393, G:Y.416, G:M.419, G:G.420, G:Q.446 IMP.39: 20 residues within 4Å: Chain H: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.40 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:S.73, H:R.327, H:R.327, H:S.334, H:D.369, H:G.371, H:G.392, H:S.393, H:Y.416, H:M.419, H:G.420, H:S.421, H:Q.446

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

NAD.5: 15 residues within 4Å: Chain A: T.257, H.258, D.279, S.280, S.281, F.287, G.329, M.330, C.336, T.338, M.419, G.420, Q.446 Chain D: Q.474 Ligands: IMP.4 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Q.446 Hydrogen bonds: A:T.257, A:T.257, A:D.279, A:S.281, A:G.329, A:Q.446, D:Q.474, D:Q.474 pi-Stacking: A:H.258, A:F.287 NAD.10: 17 residues within 4Å: Chain A: Q.474 Chain B: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.9 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:Q.474, A:Q.474, B:T.257, B:T.257, B:E.259, B:D.279, B:S.281, B:G.331 Hydrophobic interactions: B:Q.446 Salt bridges: B:H.258 pi-Stacking: B:H.258, B:F.287, B:F.287 NAD.15: 15 residues within 4Å: Chain B: Q.474 Chain C: T.257, H.258, E.259, D.279, S.280, S.281, F.287, G.329, M.330, T.338, M.419, G.420, Q.446 Ligands: IMP.14 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.446 Hydrogen bonds: C:T.257, C:T.257, C:E.259, C:D.279, C:S.281, C:G.329, C:Q.446, B:Q.474, B:Q.474 Salt bridges: C:H.258 pi-Stacking: C:H.258, C:F.287, C:F.287 NAD.20: 15 residues within 4Å: Chain C: Q.474 Chain D: T.257, H.258, D.279, S.280, S.281, F.287, G.329, M.330, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.19 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.446 Hydrogen bonds: D:T.257, D:T.257, D:D.279, D:S.281, D:G.329, D:Q.446, C:Q.474, C:Q.474 Salt bridges: D:H.258 pi-Stacking: D:H.258, D:F.287, D:F.287 NAD.25: 16 residues within 4Å: Chain E: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, C.336, T.338, M.419, G.420, Q.446 Chain H: Q.474 Ligands: IMP.24 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:Q.446 Hydrogen bonds: E:T.257, E:H.258, E:D.279, E:S.281, E:G.329, E:G.331, E:Q.446, H:Q.474, H:Q.474 pi-Stacking: E:H.258, E:F.287, E:F.287 NAD.30: 16 residues within 4Å: Chain E: Q.474 Chain F: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.29 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Q.446 Hydrogen bonds: F:T.257, F:D.279, F:S.281, F:G.329, F:Q.446, E:Q.474, E:Q.474 Salt bridges: F:H.258 pi-Stacking: F:H.258, F:F.287, F:F.287 NAD.35: 16 residues within 4Å: Chain F: Q.474 Chain G: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.34 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:Q.446 Hydrogen bonds: G:T.257, G:D.279, G:S.281, G:G.329, G:Q.446, F:Q.474, F:Q.474 Salt bridges: G:H.258 pi-Stacking: G:H.258, G:F.287, G:F.287 NAD.40: 13 residues within 4Å: Chain G: Q.474 Chain H: T.257, H.258, D.279, S.280, S.281, F.287, G.331, C.336, T.338, M.419, G.420 Ligands: IMP.39 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:T.257, H:S.281, H:G.331, H:T.338, H:T.338, H:Q.446, G:Q.474, G:Q.474 Salt bridges: H:H.258 pi-Stacking: H:H.258, H:F.287, H:F.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Neill, A.G. et al., Neurodevelopmental disorder mutations in the purine biosynthetic enzyme IMPDH2 disrupt its allosteric regulation. J.Biol.Chem. (2023)

Release Date

2023-04-19

Peptides

Inosine-5'-monophosphate dehydrogenase 2: 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 2

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