SMTL ID : 9b2z.1

Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 12 residues within 4Å: Chain A: L.158, V.161, K.181, R.183, A.240, L.242, A.243, G.244, T.245, Y.281, Y.286, H.287 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.158, A:R.183, A:R.183, A:G.244, A:T.245, A:T.245 Salt bridges: A:K.181, A:H.287 pi-Stacking: A:Y.286, A:Y.286

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain B: Q.137, D.154 Ligands: ATP.4 No protein-ligand interaction detected (PLIP)

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.3: 16 residues within 4Å: Chain B: G.15, M.16, P.32, I.34, Q.59, R.62, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Ligands: ATP.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.32, B:P.32, B:I.34, B:Y.69 Hydrogen bonds: B:Y.69, B:D.157, B:R.210 Salt bridges: B:R.210

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

ATP.4: 21 residues within 4Å: Chain B: N.12, G.13, S.14, G.15, M.16, K.18, G.74, G.156, D.157, G.158, V.159, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306 Ligands: CA.2, LAB.3 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:M.16, B:M.16, B:G.74, B:D.157, B:D.157, B:D.157, B:G.158, B:V.159, B:V.159, B:K.213, B:G.302, B:M.305 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cryo-EM Detection of AMPylated Histidine Implies Covalent Catalysis in AMPylation Mediated by a Bacterial Effector. J.Mol.Biol. (2024)

Release Date

2025-01-08

Peptides

Type IV secretion protein Dot: A
Actin, cytoplasmic 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type IV secretion protein Dot

Actin, cytoplasmic 1

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