SMTL ID : 8br1.2 (1 other biounit)

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-mer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.74, G.156, D.157, G.158, V.159, G.182, R.183, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.2, LAB.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:L.16, A:L.16, A:G.156, A:D.157, A:D.157, A:G.158, A:V.159, A:V.159, A:K.213, A:E.214, A:G.302 Water bridges: A:K.18, A:K.18, A:K.18, A:Q.137, A:D.154 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: D.215, D.217, H.303 Ligands: 3AT.4, MG.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.10 MG.6: 4 residues within 4Å: Chain B: D.215, D.217 Ligands: 3AT.4, MG.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.215, B:D.217, H2O.9

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.3: 15 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 Ligands: ATP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.32, A:I.34, A:I.34, A:Q.59, A:Y.69, A:E.207 Hydrogen bonds: A:D.157, A:R.210, A:K.213 Water bridges: A:R.210 Salt bridges: A:R.210

1 x 3AT: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

3AT.4: 19 residues within 4Å: Chain B: R.60, K.78, L.80, K.83, 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 Ligands: MG.5, MG.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.80 Hydrogen bonds: B:K.83, B:S.86, B:S.86, B:M.276, B:G.304, B:N.309 Water bridges: B:R.60, B:R.60, B:R.60, B:K.85, B:K.85, B:K.85, B:K.104, B:D.215, B:D.215, B:D.217, B:H.303 Salt bridges: B:R.60, B:R.60, B:K.78, B:K.78, B:K.78, B:K.85, B:K.85, B:K.104, B:K.104

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 7 residues within 4Å: Chain B: S.68, L.69, S.72, Y.75, N.135, R.138, E.141 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.68, B:S.72, B:Y.75, B:Y.75, B:N.135, B:R.138, B:E.141, B:E.141 Water bridges: B:N.135

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Actin, alpha skeletal muscle, intermediate form

Putative Adenylate cyclase

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