SMTL ID : 6ua2.1

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Bent (2/4 compressed, 2/4 extended) segment reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

GTP.1: 13 residues within 4Å: Chain A: Y.115, E.116, Q.117, P.123, K.139, F.144, C.145, G.146, S.164, S.165, K.213, T.230 Ligands: ATP.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.115, A:Q.117, A:C.145, A:G.146, A:G.146, A:G.146, A:S.164, A:S.164, A:S.164, A:S.165, A:S.165, A:T.230, A:T.230 Salt bridges: A:K.139, A:K.213 GTP.2: 4 residues within 4Å: Chain A: K.200, D.231, N.235, K.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.235, A:N.235 Salt bridges: A:D.231 GTP.6: 13 residues within 4Å: Chain B: Y.115, E.116, Q.117, P.123, V.124, F.144, C.145, G.146, I.147, S.164, S.165, T.230 Ligands: ATP.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.115, B:Q.117, B:Q.117, B:V.124, B:C.145, B:C.145, B:G.146, B:S.165, B:T.230, B:T.230 Salt bridges: B:K.213 pi-Stacking: B:F.144, B:F.144 GTP.7: 8 residues within 4Å: Chain B: L.199, K.200, D.231, L.232, K.234, N.235, K.243, K.247 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.200, B:K.200, B:D.231, B:D.231, B:K.234, B:K.247 Salt bridges: B:D.231 pi-Cation interactions: B:K.247 GTP.19: 15 residues within 4Å: Chain I: Y.115, E.116, Q.117, P.123, V.124, K.139, G.143, F.144, C.145, G.146, S.164, S.165, K.213, T.230 Ligands: ATP.21 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:Y.115, I:Q.117, I:C.145, I:G.146, I:G.146, I:G.146, I:S.164, I:S.165, I:S.165, I:S.165, I:T.230 Salt bridges: I:K.139, I:K.213 GTP.20: 4 residues within 4Å: Chain I: K.200, D.231, N.235, K.247 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:D.231 GTP.24: 14 residues within 4Å: Chain J: Y.115, E.116, Q.117, P.123, V.124, F.144, C.145, G.146, I.147, S.164, S.165, A.228, T.230 Ligands: ATP.26 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:Q.117, J:V.124, J:C.145, J:C.145, J:G.146, J:S.165, J:S.165, J:S.165, J:T.230, J:T.230 pi-Stacking: J:F.144, J:F.144 GTP.25: 8 residues within 4Å: Chain J: L.199, K.200, D.231, L.232, K.234, N.235, K.243, K.247 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:K.200, J:D.231, J:K.234, J:K.247 Salt bridges: J:D.231 pi-Cation interactions: J:K.247

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

ATP.3: 11 residues within 4Å: Chain A: S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, K.213 Chain J: R.166 Ligands: GTP.1 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:S.164, A:S.164, A:S.165, A:S.165, A:V.191, A:V.191, A:K.213 Salt bridges: A:R.166, A:R.166, A:K.213, A:K.213, J:R.166, J:R.166 ATP.8: 14 residues within 4Å: Chain B: S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Chain I: R.166, K.210 Ligands: GTP.6, ATP.21 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain I Hydrogen bonds: B:S.164, B:S.164, B:S.165, B:S.165, B:S.165, B:R.166, B:V.191, B:V.191, B:K.213, I:K.210 Salt bridges: B:R.166, B:R.166, B:R.166, B:K.213, B:K.213, I:R.166 ATP.11: 17 residues within 4Å: Chain C: I.162, I.163, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Chain L: R.166 Ligands: ATP.12, ATP.15 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain L Hydrogen bonds: C:S.164, C:S.164, C:S.165, C:S.165, C:R.166, C:D.167, C:D.167, C:V.191, C:V.191, C:K.211, C:G.212 Salt bridges: C:R.166, C:R.229, C:R.229, C:R.229, L:R.166 pi-Cation interactions: C:K.211 ATP.12: 16 residues within 4Å: Chain C: I.120, T.121, D.122, P.123, V.124, G.143, F.144, C.145, G.146, S.165, K.213, I.226, A.228, R.229, T.230 Ligands: ATP.11 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.122, C:V.124, C:C.145, C:G.146, C:K.213, C:R.229, C:T.230, C:T.230 Salt bridges: C:K.213, C:R.229 ATP.15: 18 residues within 4Å: Chain C: R.166, R.229 Chain L: I.162, I.163, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, S.209, K.211, G.212, K.213 Ligands: ATP.11, ATP.34 17 PLIP interactions: 12 interactions with chain L, 5 interactions with chain C Hydrogen bonds: L:I.162, L:S.164, L:S.164, L:S.164, L:S.165, L:V.191, L:S.209, L:S.209, L:G.212 Salt bridges: L:R.166, L:R.166, L:R.166, C:R.166, C:R.166, C:R.166, C:R.229, C:R.229 ATP.16: 15 residues within 4Å: Chain D: I.120, T.121, D.122, P.123, G.143, F.144, C.145, G.146, S.164, S.165, G.212, K.213, T.230 Chain K: R.229 Ligands: ATP.29 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.121, D:C.145, D:G.146, D:S.165, D:S.165, D:T.230, D:T.230 Salt bridges: D:K.213, D:K.213 ATP.21: 14 residues within 4Å: Chain B: R.166 Chain I: I.162, S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.8, GTP.19 11 PLIP interactions: 9 interactions with chain I, 2 interactions with chain B Hydrogen bonds: I:S.164, I:S.165, I:S.165, I:V.191, I:V.191, I:K.213 Salt bridges: I:R.166, I:K.213, I:K.213, B:R.166, B:R.166 ATP.26: 14 residues within 4Å: Chain A: R.166, K.210 Chain J: S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: GTP.24 18 PLIP interactions: 14 interactions with chain J, 4 interactions with chain A Hydrogen bonds: J:S.164, J:S.164, J:S.165, J:S.165, J:S.165, J:R.166, J:V.191, J:V.191, J:K.213, A:R.166, A:K.210 Salt bridges: J:R.166, J:R.166, J:R.166, J:K.213, J:K.213, A:R.166, A:K.210 ATP.29: 19 residues within 4Å: Chain D: I.162, I.163, S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, S.209, K.211, G.212, K.213, L.214 Chain K: R.166, R.229 Ligands: ATP.16, ATP.30 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain K Hydrogen bonds: D:I.162, D:S.164, D:S.164, D:S.164, D:S.165, D:R.166, D:T.185, D:V.191, D:S.209, D:S.209, D:G.212 Salt bridges: D:R.166, D:R.166, D:R.166, K:R.166, K:R.166, K:R.166, K:R.229, K:R.229 ATP.30: 16 residues within 4Å: Chain D: R.166 Chain K: I.162, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, K.213, P.215, R.229 Ligands: ATP.29, ATP.31 15 PLIP interactions: 14 interactions with chain K, 1 interactions with chain D Hydrogen bonds: K:S.164, K:S.164, K:S.164, K:S.165, K:S.165, K:R.166, K:V.191, K:V.191, K:K.211, K:G.212 Salt bridges: K:R.166, K:R.229, K:R.229, D:R.166 pi-Cation interactions: K:K.211 ATP.31: 13 residues within 4Å: Chain K: I.120, D.122, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, R.229, T.230 Ligands: ATP.30 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:V.124, K:C.145, K:G.146, K:G.146, K:K.213, K:R.229, K:T.230, K:T.230 Salt bridges: K:K.213, K:R.229 pi-Stacking: K:F.144 ATP.34: 16 residues within 4Å: Chain C: R.229 Chain L: I.120, T.121, D.122, P.123, H.142, G.143, F.144, C.145, G.146, S.164, S.165, R.166, G.212, K.213 Ligands: ATP.15 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain C Hydrogen bonds: L:T.121, L:D.122, L:C.145, L:G.146, L:S.165, L:S.165, L:S.165 Salt bridges: L:K.213, L:K.213, C:R.229

8 x IMP: INOSINIC ACID(Non-covalent)(Covalent)

IMP.4: 20 residues within 4Å: Chain A: S.73, R.327, G.333, S.334, I.335, C.336, 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.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.73, A:R.327, A:S.334, A:D.369, A:D.369, A:G.370, A:G.371, A:G.392, A:S.393, A:S.393, A:S.393, A:S.393, A:M.419, A:G.420, A:Q.446, A:Q.446 IMP.9: 17 residues within 4Å: Chain B: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, M.390, G.392, S.393, Y.416, G.418, M.419, G.420 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.73, B:R.327, B:S.334, B:C.336, B:G.370, B:G.371, B:G.392, B:S.393, B:G.420 IMP.13: 19 residues within 4Å: Chain C: R.327, G.333, S.334, I.335, C.336, 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.14 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.327, C:S.334, C:D.369, C:G.370, C:G.371, C:I.372, C:G.392, C:S.393, C:S.393, C:S.393, C:S.393, C:M.419, C:G.420, C:S.421, C:Q.446 IMP.17: 18 residues within 4Å: Chain D: 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, Q.446, G.447 Ligands: NAD.18 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.327, D:S.334, D:S.334, D:S.334, D:I.335, D:G.371, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.22: 18 residues within 4Å: Chain I: S.73, 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, Q.446, G.447 Ligands: NAD.23 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:S.73, I:S.73, I:R.327, I:S.334, I:S.334, I:D.369, I:G.370, I:G.371, I:G.392, I:S.393, I:S.393, I:Y.416, I:M.419, I:G.420, I:Q.446, I:Q.446 IMP.27: 18 residues within 4Å: Chain J: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.391, G.392, S.393, Y.416, G.418, M.419, G.420 Ligands: NAD.28 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:S.73, J:S.73, J:R.327, J:S.334, J:C.336, J:D.369, J:D.369, J:G.370, J:G.371, J:G.392, J:S.393, J:Y.416, J:G.418, J:G.420 IMP.32: 19 residues within 4Å: Chain K: R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, I.372, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.33 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:R.327, K:S.334, K:D.369, K:G.370, K:G.371, K:I.372, K:G.392, K:S.393, 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.35: 18 residues within 4Å: Chain L: 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, Q.446, G.447 Ligands: NAD.36 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:R.327, L:R.327, L:S.334, L:S.334, L:S.334, L:I.335, L:D.369, L:G.370, L:G.371, L:I.372, L:Y.416, L:M.419, L:G.420, L:Q.446

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

NAD.5: 14 residues within 4Å: Chain A: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, M.419, G.420, Q.446 Chain D: H.471 Ligands: IMP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.257, A:S.281, A:S.281, A:N.308, A:G.329 NAD.10: 16 residues within 4Å: Chain A: T.50, Q.474 Chain B: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, Q.446 Ligands: IMP.9 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:Q.474, B:T.257, B:H.258, B:E.259, B:D.279, B:S.281, B:N.308, B:G.329, B:G.331 Salt bridges: B:H.258 pi-Stacking: B:H.258, B:H.258, B:F.287, B:F.287 NAD.14: 14 residues within 4Å: Chain B: A.51, H.471, Q.474 Chain C: T.257, H.258, D.279, S.280, S.281, F.287, N.308, R.327, T.338, M.419 Ligands: IMP.13 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:Q.474, B:Q.474, C:T.257, C:T.257, C:D.279, C:S.281, C:S.281, C:N.308, C:R.327 Hydrophobic interactions: C:T.338 pi-Stacking: C:F.287 pi-Cation interactions: C:H.258 NAD.18: 13 residues within 4Å: Chain C: H.471 Chain D: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, M.419, G.420, Q.446 Ligands: IMP.17 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Q.446 Hydrogen bonds: D:T.257, D:D.279, D:S.281, D:S.281, D:N.308, D:Q.446 Salt bridges: D:H.258 pi-Stacking: D:F.287, D:F.287 pi-Cation interactions: D:H.258, D:H.258 NAD.23: 13 residues within 4Å: Chain I: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.419, G.420, Q.446 Chain L: H.471 Ligands: IMP.22 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:T.257, I:T.257, I:D.279, I:S.281, I:S.281, I:N.308, I:G.329 NAD.28: 18 residues within 4Å: Chain I: T.50, Q.474 Chain J: T.257, H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, G.331, C.336, T.338, G.420, Q.446 Ligands: IMP.27 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:T.257, J:T.257, J:D.279, J:S.281, J:N.308, J:R.327, J:G.329, J:G.331, I:Q.474 Salt bridges: J:H.258 pi-Stacking: J:H.258, J:F.287, J:F.287 pi-Cation interactions: J:H.258 NAD.33: 15 residues within 4Å: Chain J: A.51, H.471, Q.474 Chain K: T.257, H.258, D.279, S.280, S.281, F.287, N.308, R.327, M.330, T.338, M.419 Ligands: IMP.32 11 PLIP interactions: 2 interactions with chain J, 9 interactions with chain K Hydrogen bonds: J:Q.474, J:Q.474, K:T.257, K:D.279, K:S.281, K:S.281, K:N.308, K:R.327 Hydrophobic interactions: K:T.338 pi-Stacking: K:F.287 pi-Cation interactions: K:H.258 NAD.36: 13 residues within 4Å: Chain K: H.471 Chain L: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, M.419, G.420, Q.446 Ligands: IMP.35 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:T.257, L:D.279, L:D.279, L:S.281, L:S.281, L:N.308, L:Q.446 Salt bridges: L:H.258 pi-Stacking: L:F.287, L:F.287 pi-Cation interactions: L:H.258, L: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
B

C
C

D
D

E
M

F
N

G
O

H
P

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Inosine-5'-monophosphate dehydrogenase 2

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