SMTL ID : 7mir.1

Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: H.397, R.405, D.407, R.410, Y.411, Q.412, V.415, Q.422, F.423, Q.424, L.425, G.426, R.427, N.638, R.639, E.640 Chain C: E.635 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.405, A:D.407, A:D.407, A:Q.412, A:Q.422, A:Q.422, A:Q.424, A:L.425, A:G.426, C:E.635 Salt bridges: A:H.397, A:R.405 pi-Stacking: A:H.397, A:H.397

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Y.437, N.439, R.441, D.447 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.447 MG.3: 4 residues within 4Å: Chain A: K.272, D.447, D.450 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.447, A:D.447, A:D.450

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

ATP.4: 15 residues within 4Å: Chain A: Q.255, G.256, R.257, T.258, K.272, K.275, R.332, L.336, Y.357, Y.437, N.439, R.441, D.447 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.256, A:R.332, A:R.332, A:Y.357 Salt bridges: A:R.257, A:R.257, A:K.272, A:K.272, A:K.275, A:R.441 pi-Stacking: A:Y.437, A:Y.437

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain B: D.22, D.24, D.26, T.28, I.29 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.22, B:D.24, B:D.26, B:T.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osinski, A. et al., Structural and mechanistic basis for protein glutamylation by the kinase fold. Mol.Cell (2021)

Release Date

2021-08-18

Peptides

Calmodulin-dependent glutamylase SidJ: A
Calmodulin-2: B
Ubiquitinating/deubiquitinating enzyme SdeA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Calmodulin-dependent glutamylase SidJ

Calmodulin-2

Ubiquitinating/deubiquitinating enzyme SdeA

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