SMTL ID : 8gm5.1

Functional construct of the Eukaryotic elongation factor 2 kinase bound to Calmodulin, ADP and to the A-484954 inhibitor and showing two conformations for the 498-520 loop

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: R.45, R.47, Y.48, L.56, K.82, S.84, N.85, F.86, Y.98, Q.142, H.161 Chain B: R.90, G.96, N.97, G.98 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.47, A:N.85, A:F.86, A:Y.98, A:Q.142, A:Q.142 Water bridges: A:R.45, A:R.47, B:R.90, B:R.90 Salt bridges: A:R.45, A:R.45, A:R.47, A:K.82, A:K.82, A:H.161, B:R.90, B:R.90 pi-Cation interactions: A:R.47, A:R.47

1 x EKI: 7-amino-1-cyclopropyl-3-ethyl-2,4-dioxo-1,2,3,4-tetrahydropyrido[2,3-d]pyrimidine-6-carboxamide(Non-covalent)

EKI.2: 14 residues within 4Å: Chain A: F.69, G.70, R.71, R.75, C.77, V.99, K.101, E.160, H.161, Y.162, I.163, Y.167, T.214, D.215 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.69, A:R.75, A:Y.167, A:T.214 Hydrogen bonds: A:K.101, A:E.160, A:H.161, A:I.163, A:I.163, A:Y.167, A:T.214 pi-Stacking: A:Y.167

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.191, H.243, C.245, C.249 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.191, A:H.243, A:C.245, A:C.249

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain B: D.93, D.95, N.97, Y.99, E.104 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.93, B:D.95, B:Y.99, B:E.104, H2O.5 CA.5: 5 residues within 4Å: Chain B: D.129, D.131, D.133, Q.135, E.140 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.129, B:D.131, B:D.133, B:Q.135, B:E.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piserchio, A. et al., Structure of the complex between calmodulin and a functional construct of eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor. J.Biol.Chem. (2023)

Release Date

2023-05-31

Peptides

Eukaryotic elongation factor 2 kinase: A
Calmodulin-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Eukaryotic elongation factor 2 kinase

Calmodulin-1

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