SMTL ID : 6u9o.1

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Fully compressed filament segment reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

GTP.1: 16 residues within 4Å: Chain A: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.124, A:C.145, A:G.146, A:S.165, A:K.213, A:K.213, A:T.230, A:T.230, A:D.231, A:K.234 Salt bridges: A:K.139, A:K.213, A:K.213, A:K.213 GTP.2: 11 residues within 4Å: Chain A: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.116, A:N.203, A:N.203, A:N.235, A:N.235, A:K.243 Salt bridges: A:D.231, A:K.243, A:K.247, A:K.247 GTP.6: 16 residues within 4Å: Chain C: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.8 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.124, C:C.145, C:G.146, C:S.165, C:K.213, C:K.213, C:T.230, C:T.230, C:D.231, C:K.234 Salt bridges: C:K.139, C:K.213, C:K.213, C:K.213 GTP.7: 11 residues within 4Å: Chain C: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.116, C:N.203, C:N.203, C:N.235, C:N.235, C:K.243 Salt bridges: C:D.231, C:K.243, C:K.247, C:K.247 GTP.11: 16 residues within 4Å: Chain E: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.13 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:V.124, E:C.145, E:G.146, E:S.165, E:K.213, E:K.213, E:T.230, E:T.230, E:D.231, E:K.234 Salt bridges: E:K.139, E:K.213, E:K.213, E:K.213 GTP.12: 11 residues within 4Å: Chain E: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:E.116, E:N.203, E:N.203, E:N.235, E:N.235, E:K.243 Salt bridges: E:D.231, E:K.243, E:K.247, E:K.247 GTP.16: 16 residues within 4Å: Chain G: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.18 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.124, G:C.145, G:G.146, G:S.165, G:K.213, G:K.213, G:T.230, G:T.230, G:D.231, G:K.234 Salt bridges: G:K.139, G:K.213, G:K.213, G:K.213 GTP.17: 11 residues within 4Å: Chain G: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:E.116, G:N.203, G:N.203, G:N.235, G:N.235, G:K.243 Salt bridges: G:D.231, G:K.243, G:K.247, G:K.247 GTP.21: 16 residues within 4Å: Chain I: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.23 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:V.124, I:C.145, I:G.146, I:S.165, I:K.213, I:K.213, I:T.230, I:T.230, I:D.231, I:K.234 Salt bridges: I:K.139, I:K.213, I:K.213, I:K.213 GTP.22: 11 residues within 4Å: Chain I: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:N.203, I:N.203, I:N.235, I:N.235, I:K.243 Salt bridges: I:D.231, I:K.243, I:K.247, I:K.247 GTP.26: 16 residues within 4Å: Chain K: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.28 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:V.124, K:C.145, K:G.146, K:S.165, K:K.213, K:K.213, K:T.230, K:T.230, K:D.231, K:K.234 Salt bridges: K:K.139, K:K.213, K:K.213, K:K.213 GTP.27: 11 residues within 4Å: Chain K: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:N.203, K:N.203, K:N.235, K:N.235, K:K.243 Salt bridges: K:D.231, K:K.243, K:K.247, K:K.247 GTP.31: 16 residues within 4Å: Chain M: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.33 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:V.124, M:C.145, M:G.146, M:S.165, M:K.213, M:K.213, M:T.230, M:T.230, M:D.231, M:K.234 Salt bridges: M:K.139, M:K.213, M:K.213, M:K.213 GTP.32: 11 residues within 4Å: Chain M: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:N.203, M:N.203, M:N.235, M:N.235, M:K.243 Salt bridges: M:D.231, M:K.243, M:K.247, M:K.247 GTP.36: 16 residues within 4Å: Chain O: E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230, D.231, K.234 Ligands: ATP.38 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:V.124, O:C.145, O:G.146, O:S.165, O:K.213, O:K.213, O:T.230, O:T.230, O:D.231, O:K.234 Salt bridges: O:K.139, O:K.213, O:K.213, O:K.213 GTP.37: 11 residues within 4Å: Chain O: E.116, G.118, L.199, K.200, N.203, I.227, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain O Hydrogen bonds: O:N.203, O:N.203, O:N.235, O:N.235, O:K.243 Salt bridges: O:D.231, O:K.243, O:K.247, O:K.247

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

ATP.3: 15 residues within 4Å: Chain A: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Chain K: R.166 Ligands: GTP.1, ATP.28 12 PLIP interactions: 1 interactions with chain K, 11 interactions with chain A Salt bridges: K:R.166, A:R.166, A:R.166, A:R.166 Hydrogen bonds: A:S.164, A:S.165, A:S.165, A:S.165, A:R.166, A:V.191, A:K.213, A:K.213 ATP.8: 15 residues within 4Å: 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 Chain I: R.166 Ligands: GTP.6, ATP.23 12 PLIP interactions: 1 interactions with chain I, 11 interactions with chain C Salt bridges: I:R.166, C:R.166, C:R.166, C:R.166 Hydrogen bonds: C:S.164, C:S.165, C:S.165, C:S.165, C:R.166, C:V.191, C:K.213, C:K.213 ATP.13: 15 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 Chain O: R.166 Ligands: GTP.11, ATP.38 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain O Hydrogen bonds: E:S.164, E:S.165, E:S.165, E:S.165, E:R.166, E:V.191, E:K.213, E:K.213 Salt bridges: E:R.166, E:R.166, E:R.166, O:R.166 ATP.18: 15 residues within 4Å: Chain G: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Chain M: R.166 Ligands: GTP.16, ATP.33 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain M Hydrogen bonds: G:S.164, G:S.165, G:S.165, G:S.165, G:R.166, G:V.191, G:K.213, G:K.213 Salt bridges: G:R.166, G:R.166, G:R.166, M:R.166 ATP.23: 15 residues within 4Å: Chain C: R.166 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 Ligands: ATP.8, GTP.21 12 PLIP interactions: 11 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:S.164, I:S.165, I:S.165, I:S.165, I:R.166, I:V.191, I:K.213, I:K.213 Salt bridges: I:R.166, I:R.166, I:R.166, C:R.166 ATP.28: 15 residues within 4Å: Chain A: R.166 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 Ligands: ATP.3, GTP.26 12 PLIP interactions: 11 interactions with chain K, 1 interactions with chain A Hydrogen bonds: K:S.164, K:S.165, K:S.165, K:S.165, K:R.166, K:V.191, K:K.213, K:K.213 Salt bridges: K:R.166, K:R.166, K:R.166, A:R.166 ATP.33: 15 residues within 4Å: Chain G: R.166 Chain M: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.18, GTP.31 12 PLIP interactions: 11 interactions with chain M, 1 interactions with chain G Hydrogen bonds: M:S.164, M:S.165, M:S.165, M:S.165, M:R.166, M:V.191, M:K.213, M:K.213 Salt bridges: M:R.166, M:R.166, M:R.166, G:R.166 ATP.38: 15 residues within 4Å: Chain E: R.166 Chain O: I.162, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.13, GTP.36 12 PLIP interactions: 11 interactions with chain O, 1 interactions with chain E Hydrogen bonds: O:S.164, O:S.165, O:S.165, O:S.165, O:R.166, O:V.191, O:K.213, O:K.213 Salt bridges: O:R.166, O:R.166, O:R.166, E:R.166

8 x IMP: INOSINIC ACID(Covalent)

IMP.4: 20 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, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.327, A:S.334, A:S.334, A:D.369, A:G.371, A:G.392, A:S.393, A:S.393, A:M.419, A:G.420, A:S.421, A:Q.446 IMP.9: 20 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, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.327, C:S.334, C:S.334, C:D.369, C:G.371, C:G.392, C:S.393, C:S.393, C:M.419, C:G.420, C:S.421, C:Q.446 IMP.14: 20 residues within 4Å: Chain E: 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.15 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.327, E:S.334, E:S.334, E:D.369, E:G.371, E:G.392, E:S.393, E:S.393, E:M.419, E:G.420, E:S.421, E:Q.446 IMP.19: 20 residues within 4Å: Chain G: 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.20 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:R.327, G:S.334, G:S.334, G:D.369, G:G.371, G:G.392, G:S.393, G:S.393, G:M.419, G:G.420, G:S.421, G:Q.446 IMP.24: 20 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.25 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:R.327, I:S.334, I:D.369, I:G.371, I:G.392, I:S.393, I:S.393, I:S.393, I:Y.416, I:M.419, I:G.420, I:S.421, I:Q.446 IMP.29: 20 residues within 4Å: Chain K: 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.30 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:R.327, K:S.334, K:D.369, K:G.371, K:G.392, K:S.393, K:S.393, K:S.393, K:Y.416, K:M.419, K:G.420, K:S.421, K:Q.446 IMP.34: 20 residues within 4Å: Chain M: 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.35 13 PLIP interactions: 13 interactions with chain M Hydrogen bonds: M:R.327, M:S.334, M:D.369, M:G.371, M:G.392, M:S.393, M:S.393, M:S.393, M:Y.416, M:M.419, M:G.420, M:S.421, M:Q.446 IMP.39: 20 residues within 4Å: Chain O: 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.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.40 13 PLIP interactions: 13 interactions with chain O Hydrogen bonds: O:R.327, O:S.334, O:D.369, O:G.371, O:G.392, O:S.393, O:S.393, O:S.393, O:Y.416, O:M.419, O:G.420, O:S.421, O:Q.446

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

NAD.5: 17 residues within 4Å: Chain A: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain G: Q.474 Ligands: IMP.4 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:H.98, A:T.257, A:H.258, A:E.259, A:E.259, A:D.279, A:S.281, A:N.308, A:G.329, A:G.331, G:Q.474 Salt bridges: A:H.258 pi-Stacking: A:F.287, A:F.287 pi-Cation interactions: A:H.258, A:H.258 NAD.10: 17 residues within 4Å: Chain A: Q.474 Chain C: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.9 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.98, C:T.257, C:H.258, C:E.259, C:E.259, C:D.279, C:S.281, C:N.308, C:G.329, C:G.331, A:Q.474 Salt bridges: C:H.258 pi-Stacking: C:F.287, C:F.287 pi-Cation interactions: C:H.258, C:H.258 NAD.15: 17 residues within 4Å: Chain C: Q.474 Chain E: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.14 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain E Hydrogen bonds: C:Q.474, E:H.98, E:T.257, E:H.258, E:E.259, E:E.259, E:D.279, E:S.281, E:N.308, E:G.329, E:G.331 Salt bridges: E:H.258 pi-Stacking: E:F.287, E:F.287 pi-Cation interactions: E:H.258, E:H.258 NAD.20: 17 residues within 4Å: Chain E: Q.474 Chain G: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.19 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:H.98, G:T.257, G:H.258, G:E.259, G:E.259, G:D.279, G:S.281, G:N.308, G:G.329, G:G.331, E:Q.474 Salt bridges: G:H.258 pi-Stacking: G:F.287, G:F.287 pi-Cation interactions: G:H.258, G:H.258 NAD.25: 17 residues within 4Å: Chain I: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Chain O: Q.474 Ligands: IMP.24 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain O Hydrogen bonds: I:H.98, I:T.257, I:E.259, I:D.279, I:S.281, I:N.308, I:G.329, I:G.331, O:Q.474 Salt bridges: I:H.258 pi-Stacking: I:F.287, I:F.287 pi-Cation interactions: I:H.258, I:H.258 NAD.30: 17 residues within 4Å: Chain I: Q.474 Chain K: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.29 14 PLIP interactions: 13 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:H.98, K:T.257, K:E.259, K:D.279, K:S.281, K:N.308, K:G.329, K:G.331, I:Q.474 Salt bridges: K:H.258 pi-Stacking: K:F.287, K:F.287 pi-Cation interactions: K:H.258, K:H.258 NAD.35: 17 residues within 4Å: Chain K: Q.474 Chain M: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.34 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain K Hydrogen bonds: M:H.98, M:T.257, M:E.259, M:D.279, M:S.281, M:N.308, M:G.329, M:G.331, K:Q.474 Salt bridges: M:H.258 pi-Stacking: M:F.287, M:F.287 pi-Cation interactions: M:H.258, M:H.258 NAD.40: 17 residues within 4Å: Chain M: Q.474 Chain O: H.98, T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.39 14 PLIP interactions: 13 interactions with chain O, 1 interactions with chain M Hydrogen bonds: O:H.98, O:T.257, O:E.259, O:D.279, O:S.281, O:N.308, O:G.329, O:G.331, M:Q.474 Salt bridges: O:H.258 pi-Stacking: O:F.287, O:F.287 pi-Cation interactions: O:H.258, O:H.258

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
I

C
B

D
J

E
C

F
K

G
D

H
L

I
E

J
M

K
F

L
N

M
G

N
O

O
H

P
P

Inosine-5'-monophosphate dehydrogenase 2

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