SMTL ID : 6oqq.1 (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: 17 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: MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:H.492, A:R.500, A:D.502, A:D.502, A:Q.507, A:F.518, A:Q.519, A:Q.519, A:G.521 Water bridges: A:R.500, A:R.500, A:R.522 Salt bridges: A:H.492, A:R.500 pi-Stacking: A:H.492, A:H.492

1 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, N.534, R.536, D.542 Ligands: MG.3, MG.4, MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.353, A:Y.443, A:N.534 Water bridges: A:R.352, A:K.367, A:K.367 Salt bridges: A:R.352, A:K.367, A:K.367, A:K.370, A:R.536

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.352, K.367, D.542, D.545 Ligands: POP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.542, A:D.542, A:D.545 MG.4: 5 residues within 4Å: Chain A: Y.443, Y.449, F.450, R.536 Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: Q.350, Y.452, Y.532, R.536 Ligands: POP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.452 MG.6: 5 residues within 4Å: Chain A: T.493, F.495, R.500, Y.732 Ligands: AMP.1 No protein-ligand interaction detected (PLIP)

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

NA.7: 5 residues within 4Å: Chain A: H.492, T.493, R.522, Y.732, N.733 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.492, A:R.522, A:R.522, A:N.733 NA.19: 3 residues within 4Å: Chain B: A.18, D.21, N.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.24, B:N.24

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

EDO.8: 12 residues within 4Å: Chain A: A.105, R.106, R.107, V.318, L.478, R.479, G.481, I.549, Y.599, M.653 Chain B: D.23, N.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.478, A:Y.599 EDO.9: 10 residues within 4Å: Chain A: V.483, P.485, R.505, L.552, F.558, F.563, L.598, N.601, T.602, E.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.505, A:N.601 EDO.10: 7 residues within 4Å: Chain A: L.694, Q.695, Q.698, E.707, Y.708, E.709, F.710 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.698 EDO.11: 6 residues within 4Å: Chain A: N.289, K.666, Q.667, A.669, N.670, I.671 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.669 Water bridges: A:N.289, A:Q.667, A:N.670, A:I.671 EDO.12: 6 residues within 4Å: Chain A: R.636, A.639, N.640, I.671, E.672, F.675 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.636 Water bridges: A:N.640 EDO.13: 5 residues within 4Å: Chain A: T.464, E.637, N.640, V.641, T.644 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.637, A:E.637 EDO.14: 8 residues within 4Å: Chain A: K.219, S.220, I.225, H.226, H.280, L.792, D.793, K.803 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.219, A:S.220, A:S.220, A:H.226 EDO.15: 6 residues within 4Å: Chain A: H.234, N.236, R.262, D.263, F.292, E.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.262 Water bridges: A:N.236 EDO.16: 8 residues within 4Å: Chain A: I.134, K.252, A.256, T.574, F.575, F.576, D.577, N.584 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.252, A:A.256, A:N.584

2 x CA: CALCIUM ION(Non-covalent)

CA.17: 5 residues within 4Å: Chain B: D.21, D.23, N.24, N.25, S.27 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, B:D.23, B:S.27, H2O.17 CA.18: 6 residues within 4Å: Chain B: D.94, N.96, G.97, D.98, L.100, I.101 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.94, 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
A

B
B

Legionella pneumophila SidJ

Calmodulin

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