SMTL ID : 6u8r.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 20 residues within 4Å: Chain A: S.73, M.75, R.327, G.333, S.334, 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.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.73, A:N.308, A:R.327, A:R.327, A:S.334, 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.7: 21 residues within 4Å: Chain B: 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, G.447 Ligands: NAD.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.73, B:S.73, B:R.327, B:R.327, B:S.334, B:D.369, B:G.371, B:G.392, B:S.393, B:M.419, B:G.420, B:Q.446 IMP.11: 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, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.73, C:R.327, C:R.327, C:S.334, C:S.334, C:G.371, C:G.392, C:S.393, C:S.393, C:Y.416, C:M.419, C:G.420, C:Q.446 IMP.15: 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, I.372, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.16 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.73, D:S.73, D:R.327, D:R.327, D:S.334, D:G.370, D:G.371, D:I.372, D:I.372, D:G.392, D:S.393, D:S.393, D:M.419, D:G.420, D:S.421, D:Q.446 IMP.17: 21 residues within 4Å: Chain E: S.73, M.75, R.327, S.332, 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 Ligands: NAD.18 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.73, E:S.73, E:R.327, E:R.327, E:S.334, E:D.369, E:G.371, E:G.392, 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.23: 18 residues within 4Å: Chain F: M.75, R.327, G.333, S.334, C.336, D.369, G.370, G.371, M.390, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446, G.447 Ligands: NAD.24 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:R.327, 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.27: 20 residues within 4Å: Chain G: S.73, M.75, R.327, G.333, S.334, 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, G.447 Ligands: NAD.28 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.73, G:R.327, G:R.327, G:S.334, G:S.334, G:G.371, G:G.392, G:S.393, G:S.393, G:M.419, G:G.420, G:Q.446 IMP.31: 19 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, G.392, S.393, Y.416, G.418, M.419, G.420, Q.446 Ligands: NAD.32 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:R.327, H:R.327, H:S.334, 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

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

NAD.2: 17 residues within 4Å: Chain A: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, C.336, T.338, M.419, G.420, Q.446 Chain B: Q.474 Ligands: IMP.1 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Q.474, A:D.279, A:S.281, A:N.308, A:G.329, A:G.331 Hydrophobic interactions: A:T.338, A:Q.446 pi-Stacking: A:F.287, A:F.287 pi-Cation interactions: A:H.258, A:H.258 NAD.8: 17 residues within 4Å: Chain B: T.257, H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, G.331, T.338, M.419, G.420, Q.446 Chain C: Q.474 Ligands: IMP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.279, B:S.281, B:R.327, 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.12: 15 residues within 4Å: Chain C: T.257, H.258, D.279, S.280, S.281, F.287, N.308, G.329, M.330, G.331, M.419, Q.446 Chain D: A.51, Q.474 Ligands: IMP.11 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.257, C:H.258, C:D.279, C:S.280, C:S.281, C:N.308, C:G.329, C:G.331, C:Q.446, D:Q.474 pi-Stacking: C:F.287, C:F.287 pi-Cation interactions: C:H.258, C:H.258 NAD.16: 17 residues within 4Å: Chain A: Q.474 Chain D: 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.15 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.98, D:E.259, D:D.279, D:S.281, D:S.281, D:N.308, D:G.329, D:G.331, D:D.369, A:Q.474 Salt bridges: D:H.258 pi-Stacking: D:H.258, D:F.287, D:F.287 NAD.18: 16 residues within 4Å: Chain E: T.257, H.258, D.279, S.280, S.281, F.287, N.308, R.327, G.329, M.330, D.369, M.419, G.420, Q.446 Chain F: Q.474 Ligands: IMP.17 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:M.330 Hydrogen bonds: E:D.279, E:S.281, E:N.308, E:R.327, E:D.369, F:Q.474 pi-Stacking: E:F.287, E:F.287 pi-Cation interactions: E:H.258, E:H.258 NAD.24: 16 residues within 4Å: Chain F: 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 Chain G: Q.474 Ligands: IMP.23 12 PLIP interactions: 1 interactions with chain G, 11 interactions with chain F Hydrogen bonds: G:Q.474, F:D.279, F:S.281, F:N.308, F:G.329, F:G.331 Hydrophobic interactions: F:T.338 Salt bridges: F:H.258 pi-Stacking: F:F.287, F:F.287 pi-Cation interactions: F:H.258, F:H.258 NAD.28: 16 residues within 4Å: Chain G: 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 Chain H: Q.474 Ligands: IMP.27 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:T.338 Hydrogen bonds: G:T.257, G:D.279, G:S.281, G:N.308, G:G.329, G:G.331, H:Q.474 Salt bridges: G:H.258 pi-Stacking: G:H.258, G:H.258, G:F.287, G:F.287 NAD.32: 16 residues within 4Å: Chain E: Q.474 Chain H: 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, Q.446 Ligands: IMP.31 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:H.98, H:T.257, H:E.259, H:D.279, H:D.279, H:S.281, H:N.308, H:G.329, H:G.331, H:Q.446, E:Q.474 Salt bridges: H:H.258 pi-Stacking: H:H.258, H:F.287, H:F.287

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

ATP.3: 14 residues within 4Å: Chain A: I.162, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, K.213 Chain H: R.166 Ligands: ATP.4, ATP.29 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:S.164, A:S.165, A:D.167, A:V.191, A:K.213, A:K.213, H:R.166 Salt bridges: A:R.166, A:R.166, A:K.213, A:K.213, H:R.166 ATP.4: 11 residues within 4Å: Chain A: I.120, P.123, G.143, F.144, C.145, G.146, I.147, S.165, K.213, T.230 Ligands: ATP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:C.145, A:G.146, A:S.165, A:D.231 Salt bridges: A:K.139, A:K.213 pi-Stacking: A:F.144, A:F.144 ATP.5: 15 residues within 4Å: Chain B: I.162, S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Chain G: R.166, K.210 Ligands: ATP.6, ATP.25 12 PLIP interactions: 2 interactions with chain G, 10 interactions with chain B Hydrogen bonds: G:K.210, B:S.164, B:S.164, B:S.165, B:S.165, B:R.166, B:V.191, B:V.191, B:K.211, B:G.212, B:K.213 Salt bridges: G:R.166 ATP.6: 10 residues within 4Å: Chain B: P.123, F.144, C.145, G.146, S.165, K.213, I.226, A.228, T.230 Ligands: ATP.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:C.145, B:S.165, B:K.213, B:T.230, B:D.231, B:D.231 Salt bridges: B:K.213, B:K.213 pi-Stacking: B:F.144 ATP.9: 16 residues within 4Å: Chain C: 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 F: R.166, K.210 Ligands: ATP.10, ATP.21 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:S.165, C:R.166, C:R.166, C:V.191, C:V.191, C:G.212, C:K.213, F:K.210, F:K.210 Salt bridges: F:R.166 ATP.10: 12 residues within 4Å: Chain C: I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, A.228, T.230, D.231 Ligands: ATP.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:V.124, C:C.145, C:G.146, C:S.165, C:S.165, C:K.213, C:D.231 Salt bridges: C:K.213 pi-Stacking: C:F.144, C:F.144 ATP.13: 16 residues within 4Å: Chain D: I.162, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, K.213, P.215 Chain E: R.166, R.229 Ligands: ATP.14, ATP.19 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:I.162, D:S.164, D:S.165, D:S.165, D:R.166, D:D.167, D:V.191, D:K.211, D:G.212, D:K.213, D:K.213, E:R.229 Salt bridges: D:R.166, E:R.166, E:R.166, E:R.166 ATP.14: 11 residues within 4Å: Chain D: I.120, P.123, V.124, F.144, C.145, G.146, S.165, K.213, T.230, D.231 Ligands: ATP.13 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:V.124, D:V.124, D:C.145, D:G.146, D:S.165, D:S.165, D:D.231, D:D.231 Salt bridges: D:K.213, D:K.213 pi-Stacking: D:F.144 ATP.19: 14 residues within 4Å: Chain D: R.166 Chain E: I.162, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.13, ATP.20 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.164, E:S.165, E:R.166, E:D.167, E:V.191, E:K.213, E:K.213 Salt bridges: E:R.166, E:R.166, E:R.166, E:K.213, E:K.213, D:R.166 ATP.20: 10 residues within 4Å: Chain E: I.120, P.123, G.143, F.144, C.145, G.146, S.165, K.213, T.230 Ligands: ATP.19 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:C.145, E:G.146, E:S.165, E:D.231 Salt bridges: E:K.213, E:K.213 pi-Stacking: E:F.144, E:F.144 ATP.21: 14 residues within 4Å: Chain C: K.210 Chain F: I.162, S.164, S.165, R.166, T.185, D.189, L.190, V.191, K.211, G.212, K.213 Ligands: ATP.9, ATP.22 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:I.162, F:S.164, F:S.165, F:T.185, F:V.191, F:K.211, F:G.212, F:K.213, F:K.213, C:K.210, C:K.210 Salt bridges: F:R.166 ATP.22: 12 residues within 4Å: Chain F: I.120, P.123, G.143, F.144, C.145, G.146, S.165, K.213, I.226, T.230, D.231 Ligands: ATP.21 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:C.145, F:G.146, F:G.146, F:D.231 Salt bridges: F:K.213, F:K.213 pi-Stacking: F:F.144, F:F.144 ATP.25: 15 residues within 4Å: Chain B: R.166 Chain G: I.162, I.163, S.164, S.165, R.166, D.167, D.189, L.190, V.191, K.211, G.212, P.215 Ligands: ATP.5, ATP.26 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain G Salt bridges: B:R.166 Hydrogen bonds: G:S.164, G:S.165, G:R.166, G:R.166, G:D.189, G:K.211, G:G.212 ATP.26: 12 residues within 4Å: Chain G: I.120, P.123, V.124, G.143, F.144, C.145, G.146, S.165, A.228, T.230, D.231 Ligands: ATP.25 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:V.124, G:G.143, G:C.145, G:G.146, G:S.165, G:D.231 Salt bridges: G:K.139, G:K.213 pi-Stacking: G:F.144, G:F.144 ATP.29: 14 residues within 4Å: Chain A: R.166 Chain H: I.162, S.164, S.165, R.166, D.167, D.189, L.190, K.211, G.212, K.213, P.215 Ligands: ATP.3, ATP.30 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:S.164, H:S.164, H:S.165, H:S.165, H:R.166, H:D.167, H:T.185, H:G.212, H:K.213, H:K.213 Salt bridges: H:R.166, H:K.213, A:R.166, A:R.166 pi-Cation interactions: H:K.211 ATP.30: 11 residues within 4Å: Chain H: I.120, P.123, V.124, F.144, C.145, G.146, I.147, S.165, K.213, T.230 Ligands: ATP.29 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:V.124, H:V.124, H:C.145, H:G.146, H:S.165, H:T.230 Salt bridges: H:K.213, H:K.213 pi-Stacking: H:F.144, H:F.144

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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