SMTL ID : 6uc2.1

Human IMPDH2 treated with ATP 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)

GTP.1: 15 residues within 4Å: Chain A: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.117, A:V.124, A:C.145, A:G.146, A:S.165, A:S.165, A:S.165, A:T.230, A:K.234, A:K.234 Salt bridges: A:K.139, A:K.213 pi-Stacking: A:F.144, A:F.144 GTP.2: 6 residues within 4Å: Chain A: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.200, A:N.203, A:D.231, A:N.235, A:K.247 Salt bridges: A:K.200, A:K.200, A:D.231 pi-Cation interactions: A:K.247 GTP.4: 15 residues within 4Å: Chain B: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.117, B:V.124, B:C.145, B:G.146, B:S.165, B:S.165, B:S.165, B:T.230, B:K.234, B:K.234 Salt bridges: B:K.139, B:K.213 pi-Stacking: B:F.144, B:F.144 GTP.5: 6 residues within 4Å: Chain B: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.200, B:N.203, B:D.231, B:N.235, B:K.247 Salt bridges: B:K.200, B:K.200, B:D.231 pi-Cation interactions: B:K.247 GTP.7: 15 residues within 4Å: Chain C: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.117, C:V.124, C:C.145, C:G.146, C:S.165, C:S.165, C:S.165, C:T.230, C:K.234, C:K.234 Salt bridges: C:K.139, C:K.213 pi-Stacking: C:F.144, C:F.144 GTP.8: 6 residues within 4Å: Chain C: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.200, C:N.203, C:D.231, C:N.235, C:K.247 Salt bridges: C:K.200, C:K.200, C:D.231 pi-Cation interactions: C:K.247 GTP.10: 15 residues within 4Å: Chain D: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.117, D:V.124, D:C.145, D:G.146, D:S.165, D:S.165, D:S.165, D:T.230, D:K.234, D:K.234 Salt bridges: D:K.139, D:K.213 pi-Stacking: D:F.144, D:F.144 GTP.11: 6 residues within 4Å: Chain D: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.200, D:N.203, D:D.231, D:N.235, D:K.247 Salt bridges: D:K.200, D:K.200, D:D.231 pi-Cation interactions: D:K.247 GTP.13: 15 residues within 4Å: Chain E: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.117, E:V.124, E:C.145, E:G.146, E:S.165, E:S.165, E:S.165, E:T.230, E:K.234, E:K.234 Salt bridges: E:K.139, E:K.213 pi-Stacking: E:F.144, E:F.144 GTP.14: 6 residues within 4Å: Chain E: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:K.200, E:N.203, E:D.231, E:N.235, E:K.247 Salt bridges: E:K.200, E:K.200, E:D.231 pi-Cation interactions: E:K.247 GTP.16: 15 residues within 4Å: Chain F: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.18 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.117, F:V.124, F:C.145, F:G.146, F:S.165, F:S.165, F:S.165, F:T.230, F:K.234, F:K.234 Salt bridges: F:K.139, F:K.213 pi-Stacking: F:F.144, F:F.144 GTP.17: 6 residues within 4Å: Chain F: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:K.200, F:N.203, F:D.231, F:N.235, F:K.247 Salt bridges: F:K.200, F:K.200, F:D.231 pi-Cation interactions: F:K.247 GTP.19: 15 residues within 4Å: Chain G: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.21 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:Q.117, G:V.124, G:C.145, G:G.146, G:S.165, G:S.165, G:S.165, G:T.230, G:K.234, G:K.234 Salt bridges: G:K.139, G:K.213 pi-Stacking: G:F.144, G:F.144 GTP.20: 6 residues within 4Å: Chain G: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:K.200, G:N.203, G:D.231, G:N.235, G:K.247 Salt bridges: G:K.200, G:K.200, G:D.231 pi-Cation interactions: G:K.247 GTP.22: 15 residues within 4Å: Chain H: K.114, Y.115, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.165, R.229, T.230, K.234 Ligands: ATP.24 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.117, H:V.124, H:C.145, H:G.146, H:S.165, H:S.165, H:S.165, H:T.230, H:K.234, H:K.234 Salt bridges: H:K.139, H:K.213 pi-Stacking: H:F.144, H:F.144 GTP.23: 6 residues within 4Å: Chain H: L.199, K.200, N.203, D.231, N.235, K.247 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:K.200, H:N.203, H:D.231, H:N.235, H:K.247 Salt bridges: H:K.200, H:K.200, H:D.231 pi-Cation interactions: H:K.247

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

ATP.3: 11 residues within 4Å: Chain A: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.164, A:S.165, A:S.165, A:R.166, A:R.166, A:D.167, A:V.191, A:K.213 Salt bridges: A:R.166, A:R.166, A:R.166, A:K.211, A:K.213, A:K.213, F:R.229 pi-Cation interactions: A:K.211 ATP.6: 11 residues within 4Å: Chain B: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.4 16 PLIP interactions: 1 interactions with chain E, 15 interactions with chain B Salt bridges: E:R.229, B:R.166, B:R.166, B:R.166, B:K.211, B:K.213, B:K.213 Hydrogen bonds: B:S.164, B:S.165, B:S.165, B:R.166, B:R.166, B:D.167, B:V.191, B:K.213 pi-Cation interactions: B:K.211 ATP.9: 11 residues within 4Å: Chain C: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.7 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:S.164, C:S.165, C:S.165, C:R.166, C:R.166, C:D.167, C:V.191, C:K.213 Salt bridges: C:R.166, C:R.166, C:R.166, C:K.211, C:K.213, C:K.213, H:R.229 pi-Cation interactions: C:K.211 ATP.12: 11 residues within 4Å: Chain D: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.10 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:S.164, D:S.165, D:S.165, D:R.166, D:R.166, D:D.167, D:V.191, D:K.213 Salt bridges: D:R.166, D:R.166, D:R.166, D:K.211, D:K.213, D:K.213, G:R.229 pi-Cation interactions: D:K.211 ATP.15: 11 residues within 4Å: Chain E: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.13 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.164, E:S.165, E:S.165, E:R.166, E:R.166, E:D.167, E:V.191, E:K.213 Salt bridges: E:R.166, E:R.166, E:R.166, E:K.211, E:K.213, E:K.213, B:R.229 pi-Cation interactions: E:K.211 ATP.18: 11 residues within 4Å: Chain F: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.16 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:S.164, F:S.165, F:S.165, F:R.166, F:R.166, F:D.167, F:V.191, F:K.213 Salt bridges: F:R.166, F:R.166, F:R.166, F:K.211, F:K.213, F:K.213, A:R.229 pi-Cation interactions: F:K.211 ATP.21: 11 residues within 4Å: Chain G: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.19 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:S.164, G:S.165, G:S.165, G:R.166, G:R.166, G:D.167, G:V.191, G:K.213 Salt bridges: G:R.166, G:R.166, G:R.166, G:K.211, G:K.213, G:K.213, D:R.229 pi-Cation interactions: G:K.211 ATP.24: 11 residues within 4Å: Chain H: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, K.213 Ligands: GTP.22 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:S.164, H:S.165, H:S.165, H:R.166, H:R.166, H:D.167, H:V.191, H:K.213 Salt bridges: H:R.166, H:R.166, H:R.166, H:K.211, H:K.213, H:K.213, C:R.229 pi-Cation interactions: H:K.211

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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