SMTL ID : 8g8f.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 12 residues within 4Å: Chain A: I.162, S.164, R.166, D.167, L.190, V.191, K.211, G.212, K.213, P.215 Chain G: R.166 Ligands: ATP.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain G Hydrogen bonds: A:S.164, A:R.166, A:D.167, A:D.167, A:V.191, A:V.191, A:K.211, A:G.212, A:K.213 Salt bridges: A:R.166, A:R.166, G:R.166, G:R.166, G:R.166 ATP.2: 16 residues within 4Å: Chain A: I.120, P.123, V.124, K.139, G.143, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.124, A:C.145, A:G.146, A:G.146, A:S.165, A:S.165, A:K.213, A:T.230, A:D.231 Salt bridges: A:K.139, A:K.213, A:K.213 pi-Stacking: A:F.144, A:F.144 ATP.5: 15 residues within 4Å: Chain B: I.162, S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, G.212, K.213, P.215 Chain F: R.166 Ligands: ATP.6, ATP.21 11 PLIP interactions: 2 interactions with chain F, 9 interactions with chain B Salt bridges: F:R.166, F:R.166, B:R.166, B:R.166, B:K.211 Hydrogen bonds: B:S.164, B:D.167, B:V.191, B:V.191, B:G.212, B:K.213 ATP.6: 14 residues within 4Å: Chain B: I.120, P.123, V.124, G.143, F.144, C.145, G.146, I.147, P.148, S.165, K.213, T.230, D.231 Ligands: ATP.5 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:D.231 Salt bridges: B:K.139, B:K.213, B:K.213 pi-Stacking: B:F.144 pi-Cation interactions: B:K.213 ATP.9: 14 residues within 4Å: Chain C: I.162, S.164, S.165, R.166, D.167, L.190, V.191, K.211, G.212, K.213, P.215 Chain E: R.166 Ligands: ATP.10, ATP.17 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:S.164, C:S.165, C:R.166, C:D.167, C:V.191, C:V.191, C:G.212, C:K.213, E:R.166 Salt bridges: C:R.166, E:R.166, E:R.166 ATP.10: 15 residues within 4Å: Chain C: I.120, P.123, V.124, G.143, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.9 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:V.124, C:C.145, C:G.146, C:G.146, C:S.165, C:K.213, C:T.230, C:D.231 Salt bridges: C:K.213, C:K.213 pi-Stacking: C:F.144, C:F.144 pi-Cation interactions: C:K.213 ATP.13: 14 residues within 4Å: Chain D: I.162, S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, G.212, K.213, P.215 Chain H: R.166 Ligands: ATP.14 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain H Hydrogen bonds: D:S.164, D:S.165, D:S.165, D:R.166, D:D.167, D:V.191, D:V.191, D:K.211, D:G.212, D:K.213, H:R.166 Salt bridges: D:R.166, H:R.166, H:R.166 ATP.14: 16 residues within 4Å: Chain D: I.120, P.123, V.124, K.139, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, A.228, T.230, D.231 Ligands: ATP.13 12 PLIP interactions: 12 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:D.231 Salt bridges: D:K.139, D:K.213, D:K.213 pi-Stacking: D:F.144, D:F.144 ATP.17: 15 residues within 4Å: Chain C: R.166 Chain E: I.162, S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, G.212, K.213, P.215 Ligands: ATP.9, ATP.18 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.164, E:S.165, E:S.165, E:R.166, E:D.167, E:V.191, E:V.191, E:K.211, E:G.212, E:K.213 Salt bridges: E:R.166, E:R.166, C:R.166, C:R.166 ATP.18: 16 residues within 4Å: Chain E: I.120, P.123, V.124, K.139, G.143, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.17 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:V.124, E:G.143, E:C.145, E:G.146, E:G.146, E:S.165, E:K.213, E:D.231, E:D.231 Salt bridges: E:K.139, E:K.213, E:K.213 pi-Stacking: E:F.144, E:F.144 ATP.21: 13 residues within 4Å: Chain B: R.166 Chain F: S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, K.213, P.215 Ligands: ATP.5, ATP.22 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:S.164, F:S.165, F:R.166, F:D.167, F:D.167, F:V.191, F:V.191, F:K.211, F:G.212, F:K.213 Salt bridges: F:R.166, F:R.166, B:R.166 ATP.22: 15 residues within 4Å: Chain F: I.120, P.123, V.124, G.143, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.21 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:V.124, F:C.145, F:G.146, F:G.146, F:S.165, F:K.213, F:T.230 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.144 ATP.25: 15 residues within 4Å: Chain A: R.166, K.210 Chain G: I.162, S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, G.212, K.213, P.215 Ligands: ATP.26 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:S.164, G:S.165, G:S.165, G:R.166, G:D.167, G:V.191, G:V.191, G:K.211, G:G.212, G:K.213 Salt bridges: G:R.166, G:R.166, A:R.166 ATP.26: 15 residues within 4Å: Chain G: I.120, P.123, V.124, K.139, G.143, F.144, G.146, P.148, S.165, K.213, I.226, A.228, T.230, D.231 Ligands: ATP.25 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:V.124, G:C.145, G:G.146, G:G.146, G:S.165, G:K.213, G:T.230 Salt bridges: G:K.139, G:K.213, G:K.213 pi-Stacking: G:F.144 ATP.29: 14 residues within 4Å: Chain D: R.166 Chain H: I.162, S.164, S.165, R.166, D.167, M.184, L.190, V.191, K.211, G.212, K.213, P.215 Ligands: ATP.30 14 PLIP interactions: 12 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:S.164, H:S.164, H:S.165, H:R.166, H:D.167, H:D.167, H:V.191, H:V.191, H:K.211, H:G.212, H:K.213 Salt bridges: H:R.166, D:R.166, D:R.166 ATP.30: 14 residues within 4Å: Chain H: I.120, P.123, V.124, F.144, C.145, G.146, I.147, P.148, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.29 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:V.124, H:C.145, H:G.146, H:G.146, H:K.213, H:T.230, H:T.230, H:D.231 Salt bridges: H:K.213, H:K.213 pi-Stacking: H:F.144, H:F.144

8 x IMP: INOSINIC ACID(Covalent)

IMP.3: 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, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.73, A:R.327, A:S.334, A:D.369, A:D.369, A:G.371, A:G.392, A:S.393, A:S.393, A:S.393, A:Y.416, A:M.419, A:G.420, A:Q.446 IMP.7: 20 residues within 4Å: Chain B: S.73, M.75, 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, M.419, G.420, Q.446, G.447 Ligands: NAD.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.73, B:R.327, B:S.334, B:I.337, B:D.369, B:D.369, B:G.371, B:G.392, B:S.393, B:S.393, B:S.393, B:Y.416, B:M.419, B:G.420, B:Q.446 IMP.11: 21 residues within 4Å: Chain C: S.73, M.75, 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, Q.446, G.447 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.73, C:R.327, C:S.334, C:D.369, C:D.369, C:G.371, C:G.392, C:S.393, C:S.393, C:Y.416, C:M.419, C:G.420, C:Q.446 IMP.15: 21 residues within 4Å: Chain D: S.73, M.75, 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, Q.446, G.447 Ligands: NAD.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.73, D:R.327, D:S.334, D:D.369, D:D.369, D:G.370, D:G.371, D:G.392, D:S.393, D:S.393, D:S.393, D:Y.416, D:M.419, D:G.420, D:Q.446 IMP.19: 20 residues within 4Å: Chain E: S.73, M.75, R.327, G.333, S.334, I.335, C.336, I.337, D.369, G.370, G.371, M.391, G.392, S.393, Y.416, M.419, G.420, Q.446, G.447 Ligands: NAD.20 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.73, E:R.327, E:R.327, E:S.334, E:I.337, E:G.371, E:G.392, E:S.393, E:S.393, E:M.419, E:G.420, E:Q.446 IMP.23: 20 residues within 4Å: Chain F: S.73, M.75, 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, M.419, G.420, Q.446, G.447 Ligands: NAD.24 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.73, F:S.73, F:R.327, F:S.334, F:D.369, F:G.371, F:G.392, F:S.393, F:M.419, F:G.420, F:Q.446 IMP.27: 22 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, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.28 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.73, G:S.73, G:N.308, G:R.327, G:S.334, G:D.369, G:G.371, G:G.392, G:S.393, G:M.419, G:G.420, G:Q.446 IMP.31: 20 residues within 4Å: Chain H: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.32 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:S.73, H:S.73, H:R.327, H:S.334, H:D.369, H:G.371, H:G.392, H:S.393, H:M.419, H:G.420, H:Q.446

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

NAD.4: 16 residues within 4Å: Chain A: T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, T.338, M.419, G.420, Q.446 Chain B: T.50, Q.474 Ligands: IMP.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.446 Hydrogen bonds: A:H.98, A:T.257, A:D.279, A:S.281, A:G.329, A:G.331, B:Q.474, B:Q.474 pi-Stacking: A:H.258, A:F.287, A:F.287 NAD.8: 17 residues within 4Å: Chain B: H.98, T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain C: T.50, Q.474 Ligands: IMP.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.98, B:T.257, B:D.279, B:S.281, B:S.281, B:G.329, B:G.331, C:Q.474, C:Q.474 Salt bridges: B:H.258 pi-Stacking: B:F.287, B:F.287 pi-Cation interactions: B:H.258 NAD.12: 17 residues within 4Å: Chain C: H.98, T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, C.336, M.419, G.420, Q.446 Chain D: T.50, Q.474 Ligands: IMP.11 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Q.446 Hydrogen bonds: C:H.98, C:T.257, C:D.279, C:S.281, C:G.329, C:G.331, D:Q.474 pi-Stacking: C:H.258, C:F.287, C:F.287 NAD.16: 17 residues within 4Å: Chain A: T.50, Q.474 Chain D: H.98, T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, C.336, M.419, G.420, Q.446 Ligands: IMP.15 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.98, D:T.257, D:D.279, D:S.281, D:G.329, D:G.331, A:Q.474 pi-Stacking: D:H.258, D:F.287, D:F.287 NAD.20: 16 residues within 4Å: Chain E: H.98, T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain F: T.50, Q.474 Ligands: IMP.19 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Q.446 Hydrogen bonds: E:H.98, E:T.257, E:T.257, E:D.279, E:S.281, E:G.329, E:G.331, F:Q.474 Salt bridges: E:H.258 pi-Stacking: E:H.258, E:F.287, E:F.287 NAD.24: 16 residues within 4Å: Chain F: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain G: T.50, Q.474 Ligands: IMP.23 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:H.98, F:T.257, F:T.257, F:D.279, F:S.281, F:G.329, F:G.331, G:Q.474 Salt bridges: F:H.258 pi-Stacking: F:H.258, F:F.287, F:F.287 NAD.28: 15 residues within 4Å: Chain G: T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain H: T.50, Q.474 Ligands: IMP.27 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:Q.446 Hydrogen bonds: G:H.98, G:T.257, G:T.257, G:D.279, G:S.281, G:G.329, G:G.331, H:Q.474, H:Q.474 pi-Stacking: G:H.258, G:F.287, G:F.287 NAD.32: 17 residues within 4Å: Chain E: T.50, Q.474 Chain H: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, M.419, G.420, Q.446 Ligands: IMP.31 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:Q.446 Hydrogen bonds: H:T.257, H:T.257, H:D.279, H:S.281, H:S.281, H:G.329, H:G.331, E: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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