SMTL ID : 6u8n.1

Human IMPDH2 treated with ATP, IMP, and NAD+. Fully extended filament segment reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

ATP.1: 16 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 Chain N: R.166, K.210 Ligands: ATP.2, ATP.25 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain N Hydrogen bonds: B:I.162, B:S.165, B:R.166, B:V.191, B:V.191, B:K.211, B:G.212 Salt bridges: B:R.166, B:R.166, B:R.166, N:R.166, N:R.166 ATP.2: 11 residues within 4Å: Chain B: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.124, B:V.124, B:C.145, B:G.146 pi-Stacking: B:F.144, B:F.144 ATP.5: 16 residues within 4Å: Chain D: 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 L: R.166, K.210 Ligands: ATP.6, ATP.21 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain L Hydrogen bonds: D:I.162, D:S.165, D:R.166, D:V.191, D:V.191, D:K.211, D:G.212 Salt bridges: D:R.166, D:R.166, D:R.166, L:R.166, L:R.166 ATP.6: 11 residues within 4Å: Chain D: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.5 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:V.124, D:V.124, D:C.145, D:G.146 pi-Stacking: D:F.144, D:F.144 ATP.9: 16 residues within 4Å: 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 Chain J: R.166, K.210 Ligands: ATP.10, ATP.17 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:I.162, F:S.165, F:R.166, F:V.191, F:V.191, F:K.211, F:G.212 Salt bridges: F:R.166, F:R.166, F:R.166, J:R.166, J:R.166 ATP.10: 11 residues within 4Å: Chain F: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.9 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:V.124, F:V.124, F:C.145, F:G.146 pi-Stacking: F:F.144, F:F.144 ATP.13: 16 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 Chain P: R.166, K.210 Ligands: ATP.14, ATP.29 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain P Hydrogen bonds: H:I.162, H:S.165, H:R.166, H:V.191, H:V.191, H:K.211, H:G.212 Salt bridges: H:R.166, H:R.166, H:R.166, P:R.166, P:R.166 ATP.14: 11 residues within 4Å: Chain H: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.13 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:V.124, H:V.124, H:C.145, H:G.146 pi-Stacking: H:F.144, H:F.144 ATP.17: 16 residues within 4Å: Chain F: R.166, K.210 Chain J: 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.9, ATP.18 12 PLIP interactions: 10 interactions with chain J, 2 interactions with chain F Hydrogen bonds: J:I.162, J:S.165, J:R.166, J:V.191, J:V.191, J:K.211, J:G.212 Salt bridges: J:R.166, J:R.166, J:R.166, F:R.166, F:R.166 ATP.18: 11 residues within 4Å: Chain J: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.17 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:V.124, J:V.124, J:C.145, J:G.146, J:T.230 pi-Stacking: J:F.144, J:F.144 ATP.21: 16 residues within 4Å: Chain D: 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 Ligands: ATP.5, ATP.22 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain D Hydrogen bonds: L:I.162, L:S.165, L:R.166, L:V.191, L:V.191, L:K.211, L:G.212 Salt bridges: L:R.166, L:R.166, L:R.166, D:R.166, D:R.166 ATP.22: 11 residues within 4Å: Chain L: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.21 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:V.124, L:V.124, L:C.145, L:G.146, L:T.230 pi-Stacking: L:F.144, L:F.144 ATP.25: 16 residues within 4Å: Chain B: R.166, K.210 Chain N: 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.1, ATP.26 12 PLIP interactions: 10 interactions with chain N, 2 interactions with chain B Hydrogen bonds: N:I.162, N:S.165, N:R.166, N:V.191, N:V.191, N:K.211, N:G.212 Salt bridges: N:R.166, N:R.166, N:R.166, B:R.166, B:R.166 ATP.26: 11 residues within 4Å: Chain N: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.25 7 PLIP interactions: 7 interactions with chain N Hydrogen bonds: N:V.124, N:V.124, N:C.145, N:G.146, N:T.230 pi-Stacking: N:F.144, N:F.144 ATP.29: 16 residues within 4Å: Chain H: R.166, K.210 Chain P: 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, ATP.30 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain H Hydrogen bonds: P:I.162, P:S.165, P:R.166, P:V.191, P:V.191, P:K.211, P:G.212 Salt bridges: P:R.166, P:R.166, P:R.166, H:R.166, H:R.166 ATP.30: 11 residues within 4Å: Chain P: I.120, P.123, V.124, F.144, C.145, G.146, P.148, S.165, A.228, T.230 Ligands: ATP.29 7 PLIP interactions: 7 interactions with chain P Hydrogen bonds: P:V.124, P:V.124, P:C.145, P:G.146, P:T.230 pi-Stacking: P:F.144, P:F.144

8 x IMP: INOSINIC ACID(Covalent)

IMP.3: 22 residues within 4Å: Chain B: S.73, M.75, 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 Ligands: NAD.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.327, B:S.334, B:S.334, B:D.369, B:G.370, B:G.371, B:G.392, B:S.393, B:S.393, B:M.419, B:G.420, B:S.421, B:Q.446 IMP.7: 22 residues within 4Å: Chain D: S.73, M.75, 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 Ligands: NAD.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.327, D:S.334, D:S.334, D:D.369, D:G.370, D:G.371, D:G.392, D:S.393, D:S.393, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.11: 22 residues within 4Å: Chain F: S.73, M.75, 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 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:R.327, F:S.334, F:S.334, F:D.369, F:G.370, F:G.371, F:G.392, F:S.393, F:S.393, F:M.419, F:G.420, F:S.421, F:Q.446 IMP.15: 22 residues within 4Å: Chain H: S.73, M.75, 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 Ligands: NAD.16 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:R.327, H:S.334, H:S.334, H:D.369, H:G.370, H:G.371, H:G.392, H:S.393, H:S.393, H:M.419, H:G.420, H:S.421, H:Q.446 IMP.19: 22 residues within 4Å: Chain J: S.73, M.75, 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 Ligands: NAD.20 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:R.327, J:S.334, J:S.334, J:G.370, J:G.371, J:G.392, J:S.393, J:S.393, J:Y.416, J:M.419, J:G.420, J:S.421, J:Q.446 IMP.23: 22 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, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.24 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:R.327, L:S.334, L:S.334, L:G.370, L:G.371, L:G.392, L:S.393, L:S.393, L:Y.416, L:M.419, L:G.420, L:S.421, L:Q.446 IMP.27: 22 residues within 4Å: Chain N: S.73, M.75, 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 Ligands: NAD.28 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:R.327, N:S.334, N:S.334, N:G.370, N:G.371, N:G.392, N:S.393, N:S.393, N:Y.416, N:M.419, N:G.420, N:S.421, N:Q.446 IMP.31: 22 residues within 4Å: Chain P: S.73, M.75, 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 Ligands: NAD.32 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:R.327, P:S.334, P:S.334, P:G.370, P:G.371, P:G.392, P:S.393, P:S.393, P:Y.416, P:M.419, P:G.420, P:S.421, P:Q.446

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)

NAD.4: 14 residues within 4Å: Chain B: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain D: Q.474 Ligands: IMP.3 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:M.330 Hydrogen bonds: B:D.279, B:S.281, B:N.308, B:R.327, D:Q.474, D:Q.474 Salt bridges: B:H.258 pi-Stacking: B:F.287, B:F.287 pi-Cation interactions: B:H.258, B:H.258 NAD.8: 14 residues within 4Å: Chain D: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain F: Q.474 Ligands: IMP.7 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:M.330 Hydrogen bonds: D:D.279, D:S.281, D:N.308, D:R.327, F:Q.474, F:Q.474 Salt bridges: D:H.258 pi-Stacking: D:F.287, D:F.287 pi-Cation interactions: D:H.258, D:H.258 NAD.12: 14 residues within 4Å: Chain F: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain H: Q.474 Ligands: IMP.11 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:M.330 Hydrogen bonds: F:D.279, F:S.281, F:N.308, F:R.327, H:Q.474, H:Q.474 Salt bridges: F:H.258 pi-Stacking: F:F.287, F:F.287 pi-Cation interactions: F:H.258, F:H.258 NAD.16: 14 residues within 4Å: Chain B: Q.474 Chain H: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Ligands: IMP.15 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: H:M.330 Hydrogen bonds: H:D.279, H:S.281, H:N.308, H:R.327, B:Q.474, B:Q.474 Salt bridges: H:H.258 pi-Stacking: H:F.287, H:F.287 pi-Cation interactions: H:H.258, H:H.258 NAD.20: 14 residues within 4Å: Chain J: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain L: Q.474 Ligands: IMP.19 12 PLIP interactions: 2 interactions with chain L, 10 interactions with chain J Hydrogen bonds: L:Q.474, L:Q.474, J:D.279, J:S.281, J:N.308, J:R.327 Hydrophobic interactions: J:M.330 Salt bridges: J:H.258 pi-Stacking: J:F.287, J:F.287 pi-Cation interactions: J:H.258, J:H.258 NAD.24: 14 residues within 4Å: Chain L: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain N: Q.474 Ligands: IMP.23 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain N Hydrophobic interactions: L:M.330 Hydrogen bonds: L:D.279, L:S.281, L:N.308, L:R.327, N:Q.474, N:Q.474 Salt bridges: L:H.258 pi-Stacking: L:F.287, L:F.287 pi-Cation interactions: L:H.258, L:H.258 NAD.28: 14 residues within 4Å: Chain N: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Chain P: Q.474 Ligands: IMP.27 12 PLIP interactions: 10 interactions with chain N, 2 interactions with chain P Hydrophobic interactions: N:M.330 Hydrogen bonds: N:D.279, N:S.281, N:N.308, N:R.327, P:Q.474, P:Q.474 Salt bridges: N:H.258 pi-Stacking: N:F.287, N:F.287 pi-Cation interactions: N:H.258, N:H.258 NAD.32: 14 residues within 4Å: Chain J: Q.474 Chain P: H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, Q.446 Ligands: IMP.31 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain J Hydrophobic interactions: P:M.330 Hydrogen bonds: P:D.279, P:S.281, P:N.308, P:R.327, J:Q.474, J:Q.474 Salt bridges: P:H.258 pi-Stacking: P:F.287, P:F.287 pi-Cation interactions: P:H.258, P: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
I

B
A

C
J

D
B

E
K

F
C

G
L

H
D

I
M

J
E

K
N

L
F

M
O

N
G

O
P

P
H

Inosine-5'-monophosphate dehydrogenase 2

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