SMTL ID : 8br0.1 (1 other biounit)

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin (residue Q3455 to L3863) in complex with 3'deoxyCTP and two manganese cations bound to Latrunculin-B-ADP-Mn-actin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.1: 16 residues within 4Å: Chain A: G.15, L.16, P.32, I.34, Q.59, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Chain B: P.230 Ligands: ADP.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.32, A:I.34, A:Q.59, A:Y.69, A:E.207, B:P.230 Hydrogen bonds: A:Y.69, A:D.157, A:T.186, A:R.210, A:K.213 Salt bridges: A:R.210

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 20 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.156, D.157, G.182, R.183, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: LAB.1, MN.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:G.15, A:L.16, A:L.16, A:D.157, A:D.157, A:D.157, A:K.213, A:E.214, A:G.302, A:T.303 Water bridges: A:K.18, A:K.18, A:K.18, A:K.18, A:Y.306, A:K.336 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306

3 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)

MN.3: 1 residues within 4Å: Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MN.4: 4 residues within 4Å: Chain B: D.215, D.217 Ligands: MN.5, CH1.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.215, B:D.217, H2O.9 MN.5: 5 residues within 4Å: Chain B: D.215, D.217, H.303 Ligands: MN.4, CH1.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.215, B:D.217, B:H.303, H2O.8

1 x CH1: 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CH1.6: 19 residues within 4Å: Chain B: R.60, K.78, L.80, K.85, S.86, K.104, A.214, D.215, D.217, G.275, M.276, H.303, G.304, A.305, A.308, N.309, Y.311 Ligands: MN.4, MN.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.60, B:S.86, B:D.215, B:M.276, B:A.305 Water bridges: B:S.66, B:K.78, B:K.78, B:S.86, B:K.104, B:D.306 Salt bridges: B:R.60, B:K.78, B:K.78, B:K.78, B:K.85, B:K.85, B:K.85, B:K.104, B:K.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teixeira-Nunes, M. et al., Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin. Plos Pathog. (2023)

Release Date

2023-09-20

Peptides

Actin, alpha skeletal muscle, intermediate form: A
Putative Adenylate cyclase,Profilin-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Actin, alpha skeletal muscle, intermediate form

Putative Adenylate cyclase,Profilin-1

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