SMTL ID : 7rfh.1

HUMAN RETINAL VARIANT IMPDH1(595) TREATED WITH ATP, OCTAMER-CENTERED

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: I.206, V.207, T.208, S.209, R.210, D.211, T.229, E.233, L.234, V.236, S.253, K.255, G.256, K.257, L.258, P.259 Chain H: R.210, K.254 Ligands: ATP.2, ATP.15 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:T.208, A:S.209, A:R.210, A:D.211, A:D.211, A:T.229, A:L.234, A:K.255, A:G.256, A:K.257, A:K.257, H:K.254 Salt bridges: A:R.210, A:R.210, H:R.210, H:R.210 ATP.2: 17 residues within 4Å: Chain A: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.168, A:V.168, A:S.189, A:G.190, A:K.257, A:T.274, A:D.275 Salt bridges: A:K.183, A:K.257, A:K.257 pi-Stacking: A:F.188, A:F.188 ATP.3: 19 residues within 4Å: Chain B: I.206, T.208, S.209, R.210, D.211, I.232, E.233, L.234, V.236, S.253, K.255, G.256, K.257, L.258, P.259 Chain G: R.210, K.254 Ligands: ATP.4, ATP.13 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:T.208, B:T.208, B:T.208, B:R.210, B:D.211, B:L.234, B:L.234, B:G.256, B:K.257, G:R.210 Salt bridges: B:R.210, B:R.210, B:R.210, G:R.210 ATP.4: 18 residues within 4Å: Chain B: I.164, D.166, P.167, V.168, K.183, G.187, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:V.168, B:V.168, B:S.189, B:G.190, B:K.257, B:T.274, B:T.274, B:D.275 Salt bridges: B:K.183, B:K.257, B:K.257 pi-Stacking: B:F.188, B:F.188 ATP.5: 19 residues within 4Å: Chain C: I.206, V.207, T.208, S.209, R.210, D.211, T.229, E.233, L.234, S.253, K.255, G.256, K.257, L.258, P.259 Chain F: R.210, K.254 Ligands: ATP.6, ATP.11 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:T.208, C:D.211, C:D.211, C:T.229, C:L.234, C:K.255, C:G.256, C:K.257, C:K.257, F:R.210, F:K.254 Salt bridges: C:R.210, C:R.210, C:R.210, F:R.210, F:R.210 ATP.6: 18 residues within 4Å: Chain C: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275, K.278 Ligands: ATP.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.168, C:V.168, C:S.189, C:G.190, C:K.257, C:T.274, C:D.275 Salt bridges: C:K.183, C:K.257, C:K.257 pi-Stacking: C:F.188, C:F.188 ATP.7: 20 residues within 4Å: Chain D: I.206, V.207, T.208, S.209, R.210, D.211, T.229, I.232, E.233, L.234, S.253, K.255, G.256, K.257, L.258, P.259 Chain E: R.210, K.254 Ligands: ATP.8, ATP.9 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain D Hydrogen bonds: E:K.254, D:T.208, D:D.211, D:D.211, D:T.229, D:L.234, D:G.256, D:K.257, D:K.257 Salt bridges: E:R.210, E:R.210, E:R.210, D:R.210 ATP.8: 17 residues within 4Å: Chain D: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.168, D:V.168, D:S.189, D:G.190, D:K.257, D:T.274, D:D.275 Salt bridges: D:K.183, D:K.257, D:K.257 pi-Stacking: D:F.188, D:F.188 ATP.9: 20 residues within 4Å: Chain D: R.210, K.254 Chain E: I.206, V.207, T.208, S.209, R.210, D.211, T.229, E.233, L.234, V.236, S.253, K.255, G.256, K.257, L.258, P.259 Ligands: ATP.7, ATP.10 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:T.208, E:D.211, E:D.211, E:L.234, E:K.255, E:G.256, E:K.257, E:K.257, D:K.254 Salt bridges: E:R.210, E:R.210, D:R.210, D:R.210, D:R.210 ATP.10: 17 residues within 4Å: Chain E: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.9 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:V.168, E:V.168, E:S.189, E:G.190, E:K.257, E:T.274, E:D.275 Salt bridges: E:K.183, E:K.257, E:K.257 pi-Stacking: E:F.188 ATP.11: 20 residues within 4Å: Chain C: R.210, K.254 Chain F: I.206, V.207, T.208, S.209, R.210, D.211, T.229, I.232, E.233, L.234, S.253, K.255, G.256, K.257, L.258, P.259 Ligands: ATP.5, ATP.12 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:T.208, F:T.208, F:R.210, F:D.211, F:D.211, F:T.229, F:L.234, F:L.234, F:K.255, F:G.256, F:K.257, C:R.210, C:K.254 Salt bridges: F:R.210, F:R.210, C:R.210 ATP.12: 18 residues within 4Å: Chain F: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275, K.278 Ligands: ATP.11 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:V.168, F:V.168, F:S.189, F:G.190, F:K.257, F:T.274, F:T.274, F:D.275 Salt bridges: F:K.183, F:K.257, F:K.257 pi-Stacking: F:F.188, F:F.188 ATP.13: 20 residues within 4Å: Chain B: R.210, K.254 Chain G: I.206, V.207, T.208, S.209, R.210, D.211, T.229, E.233, L.234, V.236, S.253, K.255, G.256, K.257, L.258, P.259 Ligands: ATP.3, ATP.14 15 PLIP interactions: 11 interactions with chain G, 4 interactions with chain B Hydrogen bonds: G:T.208, G:D.211, G:D.211, G:T.229, G:L.234, G:K.255, G:G.256, G:K.257, G:K.257, B:K.254 Salt bridges: G:R.210, G:R.210, B:R.210, B:R.210, B:R.210 ATP.14: 18 residues within 4Å: Chain G: I.164, D.166, P.167, V.168, K.183, G.187, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.13 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:V.168, G:V.168, G:S.189, G:G.190, G:K.257, G:T.274, G:T.274, G:D.275 Salt bridges: G:K.183, G:K.257, G:K.257 pi-Stacking: G:F.188, G:F.188 ATP.15: 21 residues within 4Å: Chain A: R.210, K.254 Chain H: I.206, V.207, T.208, S.209, R.210, D.211, T.229, I.232, E.233, L.234, V.236, S.253, K.255, G.256, K.257, L.258, P.259 Ligands: ATP.1, ATP.16 15 PLIP interactions: 11 interactions with chain H, 4 interactions with chain A Hydrogen bonds: H:T.208, H:D.211, H:D.211, H:T.229, H:L.234, H:K.255, H:G.256, H:K.257, H:K.257, A:K.254 Salt bridges: H:R.210, H:R.210, A:R.210, A:R.210, A:R.210 ATP.16: 17 residues within 4Å: Chain H: I.164, D.166, P.167, V.168, K.183, F.188, S.189, G.190, I.191, P.192, S.209, K.257, I.270, A.272, T.274, D.275 Ligands: ATP.15 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:V.168, H:V.168, H:S.189, H:G.190, H:K.257, H:T.274, H:D.275 Salt bridges: H:K.183, H:K.257, H:K.257 pi-Stacking: H:F.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burrell, A.L. et al., IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-01-12

Peptides

Isoform 5 of Inosine-5'-monophosphate dehydrogenase 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Isoform 5 of Inosine-5'-monophosphate dehydrogenase 1

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