SMTL ID : 7mis.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

ATP.1: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.256, 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

2 x MG: MAGNESIUM ION(Non-covalent)

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

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: H.397, T.398, R.427, Y.637, N.638 Ligands: AMP.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.427, A:N.638

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 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.22, B:D.24, B:D.26, B:D.26, B:T.28

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.6: 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, N.638, R.639, E.640 Chain C: E.632 Ligands: NA.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.405, A:D.407, A:Q.412, A:Q.422, A:Q.422, A:F.423, A:Q.424, A:G.426, C:E.632 Salt bridges: A:H.397, A:R.405 pi-Stacking: A:H.397, A:H.397

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: B
SdeC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Calmodulin-dependent glutamylase SidJ

Calmodulin

SdeC

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