SMTL ID : 6udq.1

Human IMPDH2 treated with ATP, IMP, and 20 mM GTP. Fully compressed filament end reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 residues within 4Å: Chain B: 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, S.421, Q.446, G.447 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.73, B:S.73, B:N.308, B:R.327, B:S.334, B:D.369, B:D.369, B:G.370, 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:S.421, B:Q.446 IMP.6: 19 residues within 4Å: Chain C: S.73, M.75, R.327, G.333, S.334, I.335, C.336, T.338, D.369, G.370, G.371, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.73, C:S.73, C:R.327, C:R.327, C:S.334, C:S.334, C:G.370, C:G.371, C:G.392, C:S.393, C:S.393, C:M.419, C:G.420, C:Q.446 IMP.9: 22 residues within 4Å: Chain E: S.73, M.75, N.308, G.333, S.334, I.335, C.336, T.338, 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 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.73, E:S.73, E:N.308, E:S.334, E:D.369, E:G.370, E:G.371, E:G.392, E:S.393, E:S.393, E:S.393, E:M.419, E:G.420, E:S.421, E:Q.446 IMP.13: 18 residues within 4Å: Chain F: S.73, M.75, G.333, S.334, I.335, C.336, T.338, D.369, G.370, G.371, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.334, F:S.334, F:T.338, F:G.370, F:G.371, F:G.392, F:S.393, F:S.393, F:M.419, F:G.420, F:Q.446 IMP.17: 22 residues within 4Å: Chain H: 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, S.421, Q.446, G.447 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:S.73, H:S.73, H:N.308, H:R.327, H:S.334, H:S.334, H:D.369, H:D.369, H:G.370, H:G.371, H:G.392, H:S.393, H:S.393, H:Y.416, H:M.419, H:G.420, H:S.421, H:Q.446 IMP.22: 16 residues within 4Å: Chain I: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, G.392, S.393, Y.416, G.420, Q.446, G.447 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:S.73, I:R.327, I:S.334, I:S.334, I:D.369, I:G.371, I:G.392, I:S.393, I:S.393, I:G.420 IMP.25: 20 residues within 4Å: Chain K: S.73, M.75, 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, S.421, Q.446, G.447 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:S.73, K:S.73, K:N.308, K:S.334, K:S.334, K:D.369, K:D.369, K:G.370, K:G.371, K:G.392, K:S.393, K:S.393, K:M.419, K:G.420, K:S.421, K:Q.446 IMP.29: 20 residues within 4Å: Chain L: S.73, M.75, R.327, G.333, S.334, I.335, C.336, T.338, D.369, G.370, G.371, I.372, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:S.73, L:S.73, L:R.327, L:S.334, L:S.334, L:D.369, L:G.371, L:G.392, L:S.393, L:S.393, L:M.419, L:G.420, L:S.421, L:Q.446

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

GTP.2: 15 residues within 4Å: Chain B: K.114, Y.115, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230, D.231, K.234 Ligands: ATP.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.114, B:Q.117, B:V.124, B:C.145, B:G.146, B:G.146, B:S.165, B:T.230, B:D.231, B:K.234 Salt bridges: B:K.213, B:K.213, B:K.213 pi-Stacking: B:F.144 GTP.3: 12 residues within 4Å: Chain B: E.116, Q.117, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.117, B:N.203, B:N.203, B:N.235 Salt bridges: B:K.247, B:K.247 GTP.7: 17 residues within 4Å: Chain C: K.114, Y.115, I.120, D.122, P.123, F.144, C.145, G.146, S.164, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.5 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:C.145, C:G.146, C:S.164, C:K.213, C:K.213, C:T.230, C:T.230 Salt bridges: C:K.213, C:K.213 pi-Stacking: C:F.144 pi-Cation interactions: C:F.144 GTP.8: 11 residues within 4Å: Chain C: E.116, Q.117, G.118, L.199, N.203, I.227, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.116, C:Q.117, C:N.203, C:A.228 Salt bridges: C:K.247, C:K.247, C:K.247 GTP.10: 15 residues within 4Å: Chain E: K.114, Y.115, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230, D.231, K.234 Ligands: ATP.12 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:K.114, E:Q.117, E:V.124, E:C.145, E:G.146, E:G.146, E:S.165, E:D.231, E:K.234 Salt bridges: E:K.213, E:K.213, E:K.213 pi-Stacking: E:F.144 GTP.11: 12 residues within 4Å: Chain E: E.116, Q.117, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.117, E:Q.117, E:N.203, E:N.235 Salt bridges: E:K.247, E:K.247 GTP.14: 19 residues within 4Å: Chain F: K.114, Y.115, Q.117, I.120, D.122, P.123, G.143, F.144, C.145, G.146, S.164, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.16 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Q.117, F:G.143, F:C.145, F:G.146, F:S.165, F:K.213, F:K.213, F:T.230, F:T.230 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.144 pi-Cation interactions: F:F.144 GTP.15: 11 residues within 4Å: Chain F: E.116, Q.117, G.118, L.199, N.203, I.227, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.116, F:Q.117, F:N.203, F:K.243 Salt bridges: F:D.231, F:K.247, F:K.247, F:K.247 GTP.18: 15 residues within 4Å: Chain H: K.114, Y.115, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230, D.231, K.234 Ligands: ATP.20 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:K.114, H:Q.117, H:V.124, H:C.145, H:G.146, H:G.146, H:S.165, H:D.231, H:K.234 Salt bridges: H:K.213, H:K.213, H:K.213 pi-Stacking: H:F.144 pi-Cation interactions: H:F.144 GTP.19: 12 residues within 4Å: Chain H: E.116, Q.117, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:Q.117, H:Q.117, H:N.203, H:N.235 Salt bridges: H:K.247, H:K.247 GTP.23: 17 residues within 4Å: Chain I: K.114, Y.115, Q.117, I.120, D.122, P.123, F.144, C.145, G.146, S.164, S.165, K.213, I.226, A.228, T.230, K.234 Ligands: ATP.21 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:K.114, I:V.124, I:C.145, I:G.146, I:K.213, I:K.213, I:T.230, I:T.230 Salt bridges: I:K.213, I:K.213 pi-Stacking: I:F.144 GTP.24: 11 residues within 4Å: Chain I: E.116, Q.117, G.118, L.199, N.203, I.227, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:E.116, I:Q.117, I:N.203, I:K.243 Salt bridges: I:D.231, I:K.247, I:K.247, I:K.247 GTP.26: 15 residues within 4Å: Chain K: K.114, Y.115, I.120, P.123, V.124, F.144, C.145, G.146, S.164, S.165, K.213, T.230, D.231, K.234 Ligands: ATP.28 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:K.114, K:Q.117, K:V.124, K:C.145, K:G.146, K:G.146, K:S.165, K:S.165, K:D.231, K:K.234 Salt bridges: K:K.213, K:K.213, K:K.213 pi-Stacking: K:F.144 GTP.27: 11 residues within 4Å: Chain K: Q.117, 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 K Hydrogen bonds: K:Q.117, K:Q.117, K:N.203 Salt bridges: K:K.247, K:K.247 GTP.30: 14 residues within 4Å: Chain L: K.114, Y.115, Q.117, I.120, P.123, F.144, C.145, G.146, K.213, I.226, T.230, D.231, K.234 Ligands: ATP.32 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:Q.117, L:V.124, L:C.145, L:G.146, L:K.213, L:K.213, L:T.230, L:T.230, L:D.231 Salt bridges: L:K.213, L:K.213 pi-Stacking: L:F.144 GTP.31: 12 residues within 4Å: Chain L: E.116, Q.117, G.118, L.199, N.203, I.227, A.228, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:E.116, L:Q.117, L:N.203, L:A.228, L:K.243 Salt bridges: L:K.247, L:K.247, L:K.247

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

ATP.4: 18 residues within 4Å: Chain B: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain C: R.166, K.210 Ligands: GTP.2, ATP.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.164, B:S.165, B:R.166, B:D.167, B:T.185, B:V.191, B:V.191, B:K.211, B:K.213, C:R.166 Salt bridges: B:R.166, B:R.166 pi-Cation interactions: B:K.211 ATP.5: 19 residues within 4Å: Chain B: R.166, K.210, R.229 Chain C: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: ATP.4, GTP.7 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.164, C:S.165, C:R.166, C:D.167, C:V.191, C:V.191, C:K.213 Salt bridges: C:R.166, C:R.166, C:R.166, B:R.166, B:R.166, B:R.229 ATP.12: 17 residues within 4Å: Chain E: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain F: K.210 Ligands: GTP.10, ATP.16 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.164, E:S.165, E:R.166, E:D.167, E:T.185, E:V.191, E:V.191, E:K.213 Salt bridges: E:R.166, E:R.166, E:R.166, E:K.213 ATP.16: 19 residues within 4Å: Chain E: R.166, K.210, R.229 Chain F: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: ATP.12, GTP.14 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:S.164, F:S.165, F:V.191, F:V.191 Salt bridges: F:R.166, F:R.166, F:R.166, E:R.166, E:R.166, E:R.229 ATP.20: 18 residues within 4Å: Chain H: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain I: R.166, K.210 Ligands: GTP.18, ATP.21 14 PLIP interactions: 12 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:S.164, H:S.165, H:S.165, H:R.166, H:D.167, H:T.185, H:V.191, H:V.191, H:K.211, I:R.166, I:R.166 Salt bridges: H:R.166, H:R.166, H:K.213 ATP.21: 19 residues within 4Å: Chain H: R.166, K.210, R.229 Chain I: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: ATP.20, GTP.23 13 PLIP interactions: 10 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:S.164, I:S.165, I:R.166, I:D.167, I:V.191, I:V.191, I:K.213 Salt bridges: I:R.166, I:R.166, I:R.166, H:R.166, H:R.166, H:R.229 ATP.28: 17 residues within 4Å: Chain K: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain L: R.166, K.210 Ligands: GTP.26 13 PLIP interactions: 12 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:S.164, K:S.165, K:S.165, K:R.166, K:D.167, K:T.185, K:V.191, K:V.191 Salt bridges: K:R.166, K:R.166, K:R.166, K:K.213, L:R.166 ATP.32: 17 residues within 4Å: Chain K: R.166, K.210 Chain L: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: GTP.30 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:S.164, L:S.165, L:R.166, L:D.167, L:V.191, L:V.191 Salt bridges: L:R.166, L:R.166, L:K.213, K:R.166

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
A

C
E

D
J

E
B

F
F

G
K

H
C

I
G

J
L

K
D

L
H

Inosine-5'-monophosphate dehydrogenase 2

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