SMTL ID : 6ua4.1

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Bent (3/4 compressed, 1/4 extended) segment reconstruction.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: K.114, Q.117, I.120, D.122, P.123, V.124, G.143, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.117, A:V.124, A:C.145, A:G.146, A:S.164, A:S.165, A:S.165, A:K.213, A:K.213, A:T.230, A:T.230, A:D.231 Salt bridges: A:K.213 pi-Stacking: A:F.144, A:F.144 GTP.2: 7 residues within 4Å: Chain A: L.199, K.200, N.203, D.231, L.232, N.235, K.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.203 Salt bridges: A:D.231 GTP.6: 15 residues within 4Å: Chain B: Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.117, B:Q.117, B:V.124, B:C.145, B:G.146, B:G.146, B:G.146, B:S.165, B:T.230, B:T.230, B:D.231 Salt bridges: B:K.213, B:K.213 pi-Stacking: B:F.144, B:F.144 GTP.7: 11 residues within 4Å: Chain B: E.116, Q.117, G.118, L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.117, B:N.203, B:N.203, B:N.235, B:K.243, B:K.247 Salt bridges: B:K.243, B:K.247 pi-Cation interactions: B:K.247 GTP.15: 15 residues within 4Å: Chain D: Y.115, E.116, Q.117, I.120, P.123, F.144, C.145, G.146, S.164, S.165, A.228, T.230, D.231, K.234 Ligands: ATP.17 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.117, D:C.145, D:G.146, D:G.146, D:S.165, D:T.230, D:T.230, D:K.234 GTP.16: 8 residues within 4Å: Chain D: L.199, K.200, N.203, D.231, L.232, N.235, K.243, K.247 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.200, D:N.203, D:N.235 Salt bridges: D:K.200, D:D.231, D:K.247 pi-Cation interactions: D:K.247 GTP.20: 16 residues within 4Å: Chain E: K.114, Y.115, E.116, Q.117, P.123, V.124, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.22 15 PLIP interactions: 15 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:G.146, E:S.165, E:S.165, E:T.230, E:T.230, E:D.231, E:D.231 pi-Stacking: E:F.144, E:F.144 GTP.21: 9 residues within 4Å: Chain E: Q.117, G.118, L.199, K.200, N.203, D.231, L.232, N.235, K.247 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Q.117, E:G.118, E:N.203, E:K.247 Salt bridges: E:K.247, E:K.247, E:K.247 pi-Cation interactions: E:K.247 GTP.25: 17 residues within 4Å: Chain F: K.114, Y.115, E.116, Q.117, I.120, P.123, V.124, F.144, C.145, G.146, S.164, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.27 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:Q.117, F:V.124, F:C.145, F:G.146, F:G.146, F:G.146, F:S.165, F:T.230, F:T.230, F:D.231, F:D.231 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.144, F:F.144 GTP.26: 10 residues within 4Å: Chain F: E.116, Q.117, G.118, L.199, K.200, N.203, D.231, N.235, K.243, K.247 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Q.117, F:N.203, F:N.203, F:N.235, F:K.247 Salt bridges: F:K.200, F:K.247, F:K.247, F:K.247 pi-Cation interactions: F:K.247 GTP.34: 13 residues within 4Å: Chain H: Y.115, E.116, Q.117, P.123, F.144, C.145, G.146, S.164, S.165, A.228, T.230, D.231 Ligands: ATP.36 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.117, H:C.145, H:G.146, H:G.146, H:G.146, H:S.164, H:S.165, H:S.165, H:S.165, H:T.230, H:T.230, H:D.231 pi-Stacking: H:F.144 pi-Cation interactions: H:F.144 GTP.35: 9 residues within 4Å: Chain H: L.199, K.200, N.203, D.231, L.232, N.235, P.239, K.243, K.247 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:K.200, H:K.200, H:N.203, H:N.235, H:P.239, H:K.243, H:K.247 Salt bridges: H:K.200, H:D.231, H:K.243, H:K.247 pi-Cation interactions: H:K.247

10 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 F: R.229 Ligands: GTP.1, ATP.27 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.164, A:S.164, A:S.165, A:D.167, A:V.191, A:K.211, A:K.213, A:K.213 Salt bridges: A:R.166, A:R.166, A:R.166, F:R.229 ATP.8: 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 E: R.166, K.233 Ligands: GTP.6, ATP.22 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:S.164, B:S.165, B:D.167, B:D.167, B:T.185, B:V.191, B:K.211, B:K.213, B:K.213, E:R.166 Salt bridges: B:R.166, B:R.166, B:R.166, B:K.213, B:K.213, E:R.166, E:R.166, E:K.233 ATP.11: 14 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, P.215 Chain H: R.166 Ligands: ATP.12 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:S.164, C:S.165, C:R.166, C:D.167, C:T.185, C:K.211, C:G.212, C:K.213, C:K.213 pi-Cation interactions: C:K.211 Salt bridges: H:R.166, H:K.233 ATP.12: 11 residues within 4Å: Chain C: I.120, D.122, P.123, G.143, F.144, C.145, G.146, A.228, R.229, T.230 Ligands: ATP.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:C.145, C:G.146, C:G.146, C:R.229, C:T.230, C:T.230 pi-Stacking: C:F.144, C:F.144 ATP.17: 16 residues within 4Å: Chain D: I.162, S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215 Chain G: R.166, K.210 Ligands: GTP.15, ATP.30 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain G Hydrogen bonds: D:S.164, D:S.165, D:V.191, D:K.213, D:K.213, G:K.210, G:K.210 Salt bridges: D:R.166, D:R.166, G:R.166, G:R.166 ATP.22: 17 residues within 4Å: Chain B: R.166, K.210, R.229 Chain E: S.164, S.165, R.166, D.167, T.185, D.189, L.190, V.191, K.211, G.212, K.213, P.215 Ligands: ATP.8, GTP.20 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:S.164, E:S.165, E:D.167, E:V.191, E:V.191, E:K.213, B:R.166 Salt bridges: E:R.166, E:R.166, E:R.166, B:R.166, B:R.229 ATP.27: 15 residues within 4Å: Chain A: R.166 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 Ligands: ATP.3, GTP.25 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:S.164, F:S.165, F:V.191, F:K.213, F:K.213, A:R.166 Salt bridges: F:R.166, F:R.166, F:R.166, F:K.213, F:K.213, A:R.166, A:K.233 ATP.30: 16 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: ATP.17, ATP.31 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain G Salt bridges: D:R.166, D:K.233 Hydrogen bonds: G:S.164, G:S.165, G:S.165, G:R.166, G:R.166, G:D.167, G:K.211, G:G.212, G:K.213, G:K.213 pi-Cation interactions: G:K.211 ATP.31: 12 residues within 4Å: Chain G: I.120, D.122, P.123, V.124, G.143, F.144, C.145, G.146, S.165, A.228, T.230 Ligands: ATP.30 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:V.124, G:C.145, G:G.146, G:S.165, G:T.230, G:T.230, G:T.230 pi-Stacking: G:F.144, G:F.144 ATP.36: 14 residues within 4Å: Chain C: R.166, K.210 Chain H: I.162, S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: GTP.34 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain C Hydrogen bonds: H:S.164, H:S.165, H:R.166, H:T.185, H:T.185, H:V.191, H:K.213, H:K.213, C:K.210, C:K.210 Salt bridges: H:R.166, C:R.166

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 22 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, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, S.421, Q.446, G.447 Ligands: NAD.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.73, A:R.327, A:S.334, A:D.369, A:G.370, A:G.371, A:G.392, A:S.393, A:S.393, A:S.393, A:M.419, A:G.420, A:S.421, A:Q.446 IMP.9: 22 residues within 4Å: Chain B: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.10 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.73, B:N.308, B:R.327, B:S.334, B:D.369, B:D.369, B:G.371, B:G.392, B:S.393, B:S.393, B:S.393, B:M.419, B:G.420, B:Q.446 IMP.13: 22 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, I.372, 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:S.73, C:S.73, C:N.308, 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.18: 21 residues within 4Å: Chain D: S.73, M.75, R.327, G.333, S.334, C.336, 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 Ligands: NAD.19 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.73, D:S.73, D:R.327, D:S.334, D:D.369, D:G.371, D:G.392, D:S.393, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.23: 20 residues within 4Å: Chain E: S.73, M.75, 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.24 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: 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:S.393, E:Y.416, E:M.419, E:G.420, E:S.421, E:Q.446 IMP.28: 20 residues within 4Å: Chain F: S.73, M.75, R.327, G.333, S.334, I.335, C.336, D.369, G.370, G.371, M.390, M.391, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446 Ligands: NAD.29 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:R.327, F:S.334, F:D.369, F:G.371, F:G.392, F:S.393, F:S.393, F:S.393, F:Y.416, F:M.419, F:G.420, F:Q.446 IMP.32: 23 residues within 4Å: Chain G: S.73, M.75, N.308, R.327, G.333, S.334, I.335, C.336, 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 Ligands: NAD.33 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:S.73, G:N.308, G:R.327, G:S.334, G:D.369, G:G.371, G:G.392, G:S.393, G:S.393, G:S.393, G:Y.416, G:M.419, G:G.420, G:S.421, G:Q.446 IMP.37: 22 residues within 4Å: Chain H: S.73, M.75, R.327, G.333, S.334, I.335, C.336, 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 Ligands: NAD.38 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.73, H:R.327, H:R.327, H:S.334, 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

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

NAD.5: 17 residues within 4Å: Chain A: 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 D: T.50, Q.474 Ligands: IMP.4 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.257, A:E.259, A:D.279, A:S.281, A:N.308, A:G.329, A:G.331, D:Q.474 Salt bridges: A:H.258 pi-Stacking: A:H.258, A:F.287, A:F.287 NAD.10: 17 residues within 4Å: Chain A: Q.474 Chain B: H.98, T.257, H.258, D.279, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Ligands: IMP.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.338, B:Q.446 Hydrogen bonds: B:H.98, B:T.257, B:T.257, B:D.279, B:S.281, B:S.281, B:N.308, B:G.331, B:Q.446, A:Q.474 Salt bridges: B:H.258 pi-Stacking: B:H.258, B:H.258, B:F.287, B:F.287 NAD.14: 18 residues within 4Å: Chain B: T.50, Q.474 Chain C: H.98, T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, D.369, M.419, G.420, Q.446 Ligands: IMP.13 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.257, C:T.257, C:H.258, C:E.259, C:D.279, C:S.281, C:G.329, C:G.331, C:Q.446, B: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.19: 16 residues within 4Å: Chain D: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, D.369, M.419, G.420, Q.446 Ligands: IMP.18 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.259, D:E.259, D:D.279, D:S.281, D:N.308, D:G.329, D:G.331 Salt bridges: D:H.258 pi-Stacking: D:F.287 pi-Cation interactions: D:H.258, D:H.258 NAD.24: 18 residues within 4Å: Chain E: T.257, H.258, E.259, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, T.338, D.369, M.419, G.420, Q.446 Chain H: Q.474 Ligands: IMP.23 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:T.338 Hydrogen bonds: E:T.257, E:E.259, E:D.279, E:S.281, E:G.329, E:G.331, H:Q.474 Salt bridges: E:H.258 pi-Stacking: E:F.287, E:F.287 pi-Cation interactions: E:H.258, E:H.258 NAD.29: 17 residues within 4Å: Chain E: Q.474 Chain F: H.98, T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, T.338, M.419, G.420, Q.446 Ligands: IMP.28 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:T.338, F:Q.446 Hydrogen bonds: F:H.98, F:T.257, F:E.259, F:D.279, F:S.281, F:G.331, E:Q.474 Salt bridges: F:H.258 pi-Stacking: F:H.258, F:F.287, F:F.287 NAD.33: 20 residues within 4Å: Chain F: T.50, 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, C.336, D.369, M.419, G.420, Q.446 Ligands: IMP.32 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:T.257, G:D.279, G:S.281, G:S.281, G:G.329, G:G.331, G:Q.446, F:Q.474 Salt bridges: G:H.258 pi-Stacking: G:F.287, G:F.287 pi-Cation interactions: G:H.258 NAD.38: 16 residues within 4Å: Chain G: Q.474 Chain H: H.98, T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, G.420, Q.446 Ligands: IMP.37 12 PLIP interactions: 1 interactions with chain G, 11 interactions with chain H Hydrogen bonds: G:Q.474, H:E.259, H:D.279, H:S.281, H:N.308, H:G.329, H:G.331 Salt bridges: H:H.258 pi-Stacking: H:F.287, H:F.287 pi-Cation interactions: H:H.258, H: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
E

F
F

G
G

H
H

I
M

J
N

K
O

L
P

M
I

N
J

O
K

P
L

Inosine-5'-monophosphate dehydrogenase 2

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