SMTL ID : 6udo.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

8 x IMP: INOSINIC ACID(Covalent)

IMP.1: 20 residues within 4Å: Chain A: 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:N.308, A:R.327, A:S.334, A:D.369, A:G.370, A:G.371, A:G.392, A:S.393, A:M.419, A:G.420, A:Q.446 IMP.5: 20 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, Q.446 13 PLIP interactions: 13 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:G.370, B:G.371, B:G.392, B:S.393, B:M.419, B:G.420, B:Q.446 IMP.9: 20 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.73, C:S.73, C:N.308, C:R.327, C:S.334, C:D.369, C:G.370, C:G.371, C:G.392, C:S.393, C:M.419, C:G.420, C:Q.446 IMP.13: 20 residues within 4Å: Chain D: 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.73, D:S.73, D:N.308, D:R.327, D:S.334, D:D.369, D:G.370, D:G.371, D:G.392, D:S.393, D:M.419, D:G.420, D:Q.446 IMP.17: 20 residues within 4Å: Chain E: 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 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.73, E:S.73, E:N.308, E:R.327, E:S.334, E:D.369, E:D.369, E:G.370, E:G.371, E:G.392, E:S.393, E:S.393, E:Y.416, E:M.419, E:G.420, E:Q.446 IMP.21: 20 residues within 4Å: Chain F: 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 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.73, F:S.73, F:N.308, F:R.327, F:S.334, F:D.369, F:D.369, F:G.370, F:G.371, F:G.392, F:S.393, F:S.393, F:Y.416, F:M.419, F:G.420, F:Q.446 IMP.25: 20 residues within 4Å: Chain G: 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 16 PLIP interactions: 16 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:D.369, G:G.370, G:G.371, G:G.392, G:S.393, G:S.393, G:Y.416, G:M.419, G:G.420, G:Q.446 IMP.29: 20 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, Q.446 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:S.73, H:S.73, H:N.308, H:R.327, 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:Q.446

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

GTP.2: 14 residues within 4Å: Chain A: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.117, A:Q.117, A:C.145, A:G.146, A:G.146, A:S.164, A:S.165, A:T.230, A:T.230 Salt bridges: A:K.213, A:K.213, A:K.213 GTP.3: 9 residues within 4Å: Chain A: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.116, A:N.203, A:N.203, A:N.235, A:K.243 Salt bridges: A:D.231, A:K.247, A:K.247 GTP.6: 14 residues within 4Å: Chain B: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.117, B:Q.117, B:C.145, B:G.146, B:G.146, B:S.164, B:S.165, B:T.230, B:T.230 Salt bridges: B:K.213, B:K.213, B:K.213 GTP.7: 9 residues within 4Å: Chain B: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.116, B:N.203, B:N.203, B:N.235, B:K.243 Salt bridges: B:D.231, B:K.247, B:K.247 GTP.10: 14 residues within 4Å: Chain C: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.12 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.117, C:Q.117, C:C.145, C:G.146, C:G.146, C:S.164, C:S.165, C:T.230, C:T.230 Salt bridges: C:K.213, C:K.213, C:K.213 GTP.11: 9 residues within 4Å: Chain C: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.116, C:N.203, C:N.203, C:N.235, C:K.243 Salt bridges: C:D.231, C:K.247, C:K.247 GTP.14: 14 residues within 4Å: Chain D: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.16 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.117, D:Q.117, D:C.145, D:G.146, D:G.146, D:S.164, D:S.165, D:T.230, D:T.230 Salt bridges: D:K.213, D:K.213, D:K.213 GTP.15: 9 residues within 4Å: Chain D: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.116, D:N.203, D:N.203, D:N.235, D:K.243 Salt bridges: D:D.231, D:K.247, D:K.247 GTP.18: 14 residues within 4Å: Chain E: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.20 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Q.117, E:Q.117, E:C.145, E:G.146, E:G.146, E:S.164, E:S.165, E:T.230, E:T.230 Salt bridges: E:K.213, E:K.213, E:K.213 GTP.19: 9 residues within 4Å: Chain E: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.203, E:N.203, E:N.235, E:K.243 Salt bridges: E:D.231, E:K.247, E:K.247 GTP.22: 14 residues within 4Å: Chain F: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.24 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Q.117, F:Q.117, F:C.145, F:G.146, F:G.146, F:S.164, F:S.165, F:T.230, F:T.230 Salt bridges: F:K.213, F:K.213, F:K.213 GTP.23: 9 residues within 4Å: Chain F: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.203, F:N.203, F:N.235, F:K.243 Salt bridges: F:D.231, F:K.247, F:K.247 GTP.26: 14 residues within 4Å: Chain G: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.28 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:Q.117, G:Q.117, G:C.145, G:G.146, G:G.146, G:S.164, G:S.165, G:T.230, G:T.230 Salt bridges: G:K.213, G:K.213, G:K.213 GTP.27: 9 residues within 4Å: Chain G: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:N.203, G:N.203, G:N.235, G:K.243 Salt bridges: G:D.231, G:K.247, G:K.247 GTP.30: 14 residues within 4Å: Chain H: K.114, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.32 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:Q.117, H:Q.117, H:C.145, H:G.146, H:G.146, H:S.164, H:S.165, H:T.230, H:T.230 Salt bridges: H:K.213, H:K.213, H:K.213 GTP.31: 9 residues within 4Å: Chain H: E.116, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:N.203, H:N.203, H:N.235, H:K.243 Salt bridges: H:D.231, H:K.247, H:K.247

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

ATP.4: 15 residues within 4Å: Chain A: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain F: R.166 Ligands: GTP.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.164, A:S.165, A:S.165, A:R.166, A:D.167, A:V.191, A:V.191, A:K.213 Salt bridges: A:R.166, A:R.166, A:K.213, F:R.166 ATP.8: 15 residues within 4Å: Chain B: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Chain E: R.166 Ligands: GTP.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.164, B:S.165, B:S.165, B:R.166, B:D.167, B:V.191, B:V.191, B:K.213 Salt bridges: B:R.166, B:R.166, B:K.213, E:R.166 ATP.12: 15 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, L.214, P.215 Chain H: R.166 Ligands: GTP.10 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:S.164, C:S.165, 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:K.213, H:R.166 ATP.16: 15 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, L.214, P.215 Chain G: R.166 Ligands: GTP.14 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain G 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.213 Salt bridges: D:R.166, D:R.166, D:K.213, G:R.166 ATP.20: 15 residues within 4Å: Chain B: R.166 Chain E: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: GTP.18 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.164, E:S.165, 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:K.213, B:R.166 ATP.24: 15 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, L.214, P.215 Ligands: GTP.22 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:S.164, F:S.165, F:S.165, F:R.166, F:D.167, F:T.185, F:V.191, F:V.191, F:K.213 Salt bridges: F:R.166, F:R.166, F:K.213, A:R.166 ATP.28: 15 residues within 4Å: Chain D: R.166 Chain G: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: GTP.26 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:S.164, G:S.165, G:S.165, G:R.166, G:D.167, G:T.185, G:V.191, G:V.191, G:K.213 Salt bridges: G:R.166, G:R.166, G:K.213, D:R.166 ATP.32: 15 residues within 4Å: Chain C: R.166 Chain H: I.162, S.164, S.165, R.166, D.167, T.185, L.190, V.191, K.211, G.212, K.213, L.214, P.215 Ligands: GTP.30 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain C 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.213 Salt bridges: H:R.166, H:R.166, H:K.213, C: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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Inosine-5'-monophosphate dehydrogenase 2

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