SMTL ID : 6oqq.2 (1 other biounit)

Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 18 residues within 4Å: Chain A: H.492, R.500, D.502, R.505, Y.506, Q.507, V.510, Q.517, F.518, Q.519, L.520, G.521, R.522, N.733, R.734, E.735 Ligands: POP.3, MG.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.500, A:D.502, A:D.502, A:Q.507, A:Q.517, A:Q.517, A:F.518, A:Q.519, A:Q.519, A:G.521 Water bridges: A:R.522 Salt bridges: A:H.492, A:R.500 pi-Stacking: A:H.492, A:H.492

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 12 residues within 4Å: Chain A: Q.350, R.352, T.353, K.367, K.370, Y.443, Y.452, N.534, R.536, D.542 Ligands: MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.443, A:N.534 Water bridges: A:R.352, A:R.352, A:T.353, A:K.367, A:K.367, A:D.542, A:D.545 Salt bridges: A:R.352, A:K.367, A:K.367, A:K.370, A:R.536 POP.3: 8 residues within 4Å: Chain A: H.492, T.493, F.495, R.500, Y.732, N.733 Ligands: AMP.1, MG.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.493, A:Y.732, A:N.733 Water bridges: A:N.733 Salt bridges: A:R.500, A:R.500

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: R.352, K.367, D.542, D.545 Ligands: POP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.542, A:D.542, A:D.545, H2O.8 MG.5: 6 residues within 4Å: Chain A: Q.350, Y.443, Y.449, F.450, R.536 Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: H.492, N.733 Ligands: AMP.1, POP.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.3

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 9 residues within 4Å: Chain A: I.134, K.252, N.253, A.256, T.574, F.575, F.576, D.577, N.584 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.574 Water bridges: A:A.256, A:N.584 EDO.8: 7 residues within 4Å: Chain A: K.260, S.303, T.304, D.307, Q.511, L.512, K.590 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.260, A:T.304, A:T.304, A:Q.511 EDO.9: 7 residues within 4Å: Chain A: D.283, E.284, R.660, T.663, L.664, P.797, G.798 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.283, A:E.284, A:P.797 EDO.10: 8 residues within 4Å: Chain A: I.134, A.256, K.260, V.515, F.575, S.585, L.586, F.587 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.260, A:L.586, A:F.587 Water bridges: A:A.256

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain B: D.21, D.23, N.25, S.27, I.28 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.21, B:D.23, B:S.27 CA.12: 5 residues within 4Å: Chain B: D.94, N.96, G.97, D.98, L.100 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.94, B:D.98, B:D.98, B:L.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Black, M.H. et al., Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science (2019)

Release Date

2019-05-15

Peptides

Legionella pneumophila SidJ: A
Calmodulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Legionella pneumophila SidJ

Calmodulin

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