SMTL ID : 6z3r.1

Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: L.1881, P.1882, T.1883, K.1884, L.1903, K.1905, Y.1943, I.1955, Q.1956, W.1957, V.1958, H.2087, D.2089, N.2090, L.2092, I.2103, D.2104, N.2106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.1883, A:K.1905, A:Q.1956, A:V.1958, A:N.2106 pi-Stacking: A:W.1957

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 10 residues within 4Å: Chain A: L.1193, K.1197, K.1241, R.1244, K.1245, K.1300, K.1334, K.1341, K.1428, Q.1933 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.1244 Salt bridges: A:K.1197, A:K.1241, A:R.1244, A:K.1245, A:K.1245, A:K.1245, A:K.1300, A:K.1300, A:K.1334, A:K.1334, A:K.1341, A:K.1341, A:K.1428, A:K.1428

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

ATP.3: 24 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, K.373, V.431, P.432, F.433, M.434, F.466 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:Q.213, C:T.215, C:T.215, C:G.216, C:K.217, C:S.218, C:M.219, C:Q.233, C:Q.241, 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., Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity. Elife (2020)

Release Date

2020-06-24

Peptides

Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1: A
Protein SMG8: B
Protein SMG9: C
Regulator of nonsense transcripts 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

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

Protein SMG8

Protein SMG9

Regulator of nonsense transcripts 1

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