SMTL ID : 6uaj.1

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free canonical octamer reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

16 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)(Covalent)

GTP.1: 13 residues within 4Å: Chain A: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.117, A:Q.117, A:Q.117, A:V.124, A:C.145, A:C.145, A:K.213, A:K.213, A:T.230, A:T.230 GTP.2: 9 residues within 4Å: Chain A: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.203, A:N.235, A:P.239, A:K.243, A:K.247 Salt bridges: A:D.231, A:K.243, A:K.243, A:K.243 pi-Cation interactions: A:K.247 GTP.6: 13 residues within 4Å: Chain B: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.117, B:Q.117, B:Q.117, B:V.124, B:C.145, B:C.145, B:K.213, B:K.213, B:T.230, B:T.230 GTP.7: 9 residues within 4Å: Chain B: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.203, B:N.235, B:P.239, B:K.243, B:K.247 Salt bridges: B:D.231, B:K.243, B:K.243, B:K.243 pi-Cation interactions: B:K.247 GTP.11: 13 residues within 4Å: Chain C: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.13 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.117, C:Q.117, C:Q.117, C:V.124, C:C.145, C:C.145, C:K.213, C:K.213, C:T.230, C:T.230 GTP.12: 9 residues within 4Å: Chain C: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.203, C:N.235, C:P.239, C:K.243, C:K.247 Salt bridges: C:D.231, C:K.243, C:K.243, C:K.243 pi-Cation interactions: C:K.247 GTP.16: 13 residues within 4Å: Chain D: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.18 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Q.117, D:Q.117, D:Q.117, D:V.124, D:C.145, D:C.145, D:K.213, D:K.213, D:T.230, D:T.230 GTP.17: 9 residues within 4Å: Chain D: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.203, D:N.235, D:P.239, D:K.243, D:K.247 Salt bridges: D:D.231, D:K.243, D:K.243, D:K.243 pi-Cation interactions: D:K.247 GTP.21: 13 residues within 4Å: Chain E: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.23 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Q.117, E:Q.117, E:Q.117, E:V.124, E:C.145, E:C.145, E:K.213, E:K.213, E:T.230, E:T.230 GTP.22: 9 residues within 4Å: Chain E: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:N.203, E:N.235, E:P.239, E:K.243, E:K.247 Salt bridges: E:D.231, E:K.243, E:K.243, E:K.243 pi-Cation interactions: E:K.247 GTP.26: 13 residues within 4Å: Chain F: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.28 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Q.117, F:Q.117, F:Q.117, F:V.124, F:C.145, F:C.145, F:K.213, F:K.213, F:T.230, F:T.230 GTP.27: 9 residues within 4Å: Chain F: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:N.203, F:N.235, F:P.239, F:K.243, F:K.247 Salt bridges: F:D.231, F:K.243, F:K.243, F:K.243 pi-Cation interactions: F:K.247 GTP.31: 13 residues within 4Å: Chain G: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.33 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:Q.117, G:Q.117, G:Q.117, G:V.124, G:C.145, G:C.145, G:K.213, G:K.213, G:T.230, G:T.230 GTP.32: 9 residues within 4Å: Chain G: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:N.203, G:N.235, G:P.239, G:K.243, G:K.247 Salt bridges: G:D.231, G:K.243, G:K.243, G:K.243 pi-Cation interactions: G:K.247 GTP.36: 13 residues within 4Å: Chain H: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.38 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:Q.117, H:Q.117, H:Q.117, H:V.124, H:C.145, H:C.145, H:K.213, H:K.213, H:T.230, H:T.230 GTP.37: 9 residues within 4Å: Chain H: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:N.203, H:N.235, H:P.239, H:K.243, H:K.247 Salt bridges: H:D.231, H:K.243, H:K.243, H:K.243 pi-Cation interactions: H:K.247

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

ATP.3: 14 residues within 4Å: Chain A: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Chain F: R.229 Ligands: GTP.1 11 PLIP interactions: 1 interactions with chain F, 10 interactions with chain A Salt bridges: F:R.229, A:R.166, A:R.166, A:R.166 Hydrogen bonds: A:S.164, A:S.165, A:R.166, A:R.166, A:V.191, A:K.213, A:R.229 ATP.8: 14 residues within 4Å: Chain B: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Chain E: R.229 Ligands: GTP.6 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain B Salt bridges: E:R.229, B:R.166, B:R.166, B:R.166 Hydrogen bonds: B:S.164, B:S.165, B:R.166, B:R.166, B:V.191, B:K.213, B:R.229 ATP.13: 14 residues within 4Å: Chain C: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Chain H: R.229 Ligands: GTP.11 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:S.164, C:S.165, C:R.166, C:R.166, C:V.191, C:K.213, C:R.229 Salt bridges: C:R.166, C:R.166, C:R.166, H:R.229 ATP.18: 14 residues within 4Å: Chain D: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Chain G: R.229 Ligands: GTP.16 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:S.164, D:S.165, D:R.166, D:R.166, D:V.191, D:K.213, D:R.229 Salt bridges: D:R.166, D:R.166, D:R.166, G:R.229 ATP.23: 14 residues within 4Å: Chain B: R.229 Chain E: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Ligands: GTP.21 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.164, E:S.165, E:R.166, E:R.166, E:V.191, E:K.213, E:R.229 Salt bridges: E:R.166, E:R.166, E:R.166, B:R.229 ATP.28: 14 residues within 4Å: Chain A: R.229 Chain F: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Ligands: GTP.26 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain F Salt bridges: A:R.229, F:R.166, F:R.166, F:R.166 Hydrogen bonds: F:S.164, F:S.165, F:R.166, F:R.166, F:V.191, F:K.213, F:R.229 ATP.33: 14 residues within 4Å: Chain D: R.229 Chain G: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Ligands: GTP.31 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:S.164, G:S.165, G:R.166, G:R.166, G:V.191, G:K.213, G:R.229 Salt bridges: G:R.166, G:R.166, G:R.166, D:R.229 ATP.38: 14 residues within 4Å: Chain C: R.229 Chain H: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Ligands: GTP.36 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:S.164, H:S.165, H:R.166, H:R.166, H:V.191, H:K.213, H:R.229 Salt bridges: H:R.166, H:R.166, H:R.166, C:R.229

8 x IMP: INOSINIC ACID(Non-covalent)

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

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

NAD.5: 17 residues within 4Å: Chain A: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Chain D: I.47, Q.474 Ligands: IMP.4 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain A Hydrogen bonds: D:Q.474, A:T.257, A:E.259, A:D.279, A:S.281, A:N.308, A:D.369 Salt bridges: A:H.258 pi-Stacking: A:H.258, A:H.258, A:F.287, A:F.287 NAD.10: 17 residues within 4Å: Chain A: I.47, Q.474 Chain B: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.9 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.257, B:E.259, B:D.279, B:S.281, B:N.308, B:D.369, A:Q.474 Salt bridges: B:H.258 pi-Stacking: B:H.258, B:H.258, B:F.287, B:F.287 NAD.15: 17 residues within 4Å: Chain B: I.47, Q.474 Chain C: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.14 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.257, C:E.259, C:D.279, C:S.281, C:N.308, C:D.369, B:Q.474 Salt bridges: C:H.258 pi-Stacking: C:H.258, C:H.258, C:F.287, C:F.287 NAD.20: 17 residues within 4Å: Chain C: I.47, Q.474 Chain D: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.19 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.257, D:E.259, D:D.279, D:S.281, D:N.308, D:D.369, C:Q.474 Salt bridges: D:H.258 pi-Stacking: D:H.258, D:H.258, D:F.287, D:F.287 NAD.25: 17 residues within 4Å: Chain E: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Chain H: I.47, Q.474 Ligands: IMP.24 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:T.257, E:E.259, E:D.279, E:S.281, E:N.308, E:D.369, H:T.50, H:Q.474 Salt bridges: E:H.258 pi-Stacking: E:H.258, E:H.258, E:F.287, E:F.287 NAD.30: 17 residues within 4Å: Chain E: I.47, Q.474 Chain F: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.29 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain F Hydrogen bonds: E:Q.474, F:T.257, F:E.259, F:D.279, F:S.281, F:N.308, F:D.369 Salt bridges: F:H.258 pi-Stacking: F:H.258, F:H.258, F:F.287, F:F.287 NAD.35: 17 residues within 4Å: Chain F: I.47, Q.474 Chain G: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.34 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain G Hydrogen bonds: F:T.50, F:Q.474, G:T.257, G:E.259, G:D.279, G:S.281, G:N.308, G:D.369 Salt bridges: G:H.258 pi-Stacking: G:H.258, G:H.258, G:F.287, G:F.287 NAD.40: 17 residues within 4Å: Chain G: I.47, Q.474 Chain H: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, R.327, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.39 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:T.257, H:E.259, H:D.279, H:S.281, H:N.308, H:D.369, G:Q.474 Salt bridges: H:H.258 pi-Stacking: H:H.258, H:H.258, H:F.287, H:F.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, M.C. et al., Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Elife (2020)

Release Date

2020-03-25

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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