SMTL ID : 7pw5.1

Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)

IHP.1: 8 residues within 4Å: Chain A: K.1382, R.1429, K.1430, K.1485, Y.1515, K.1519, K.1526, K.1613 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.1429, A:R.1429 Salt bridges: A:K.1382, A:K.1430, A:K.1430, A:K.1430, A:K.1485, A:K.1485, A:K.1519, A:K.1519, A:K.1526, A:K.1526, A:K.1613, A:K.1613

1 x 88C: 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea(Non-covalent)

88C.2: 16 residues within 4Å: Chain A: K.2151, D.2155, L.2156, D.2159, Y.2189, I.2201, Q.2202, W.2203, V.2204, A.2207, P.2209, D.2335, L.2338, I.2349, D.2350, N.2352 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.2201, A:W.2203, A:W.2203, A:P.2209, A:I.2349, A:I.2349 Hydrogen bonds: A:D.2159, A:V.2204, A:N.2352, A:N.2352 pi-Stacking: A:Y.2189, A:W.2203

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

ATP.3: 21 residues within 4Å: Chain C: L.212, Q.213, G.214, T.215, G.216, K.217, S.218, M.219, Q.233, A.240, Q.241, K.246, N.251, Q.252, T.253, P.272, N.372, P.432, F.433, M.434 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:Q.213, C:G.216, C:G.216, C:K.217, C:S.218, C:M.219, C:Q.233, C:Q.233, C:Q.241, C:Q.241, C:K.246, C:Q.252, C:T.253, C:N.372, C:P.432, C:M.434 Salt bridges: C:K.217, C:K.217 pi-Cation interactions: C:K.373

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain C: S.218, T.253 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.218, C:T.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langer, L.M. et al., Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8. Elife (2021)

Release Date

2021-12-01

Peptides

SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1: A
Protein SMG8: B
Protein SMG9: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1

Protein SMG8

Protein SMG9

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