SMTL ID : 8bjj.1

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-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 22 PLIP interactions: 22 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:E.214, A:G.302, A:T.303 Water bridges: A:K.18, A:K.18, A:K.18, A:Q.137 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.3: 18 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 C: P.230, Q.231, D.232 Ligands: ATP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.32, A:I.34, A:Y.69, A:E.207 Hydrogen bonds: A:Y.69, A:D.157, A:T.186, A:R.210, A:K.213 Salt bridges: A:R.210

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: Y.198, S.199, F.200, E.205, L.242, D.244, Q.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.199, A:S.199, A:D.244, A:Q.246 Water bridges: A:S.199 TRS.11: 8 residues within 4Å: Chain C: K.78, G.79, L.80, D.215, D.217, H.302, A.305, D.306 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.217, C:D.306 Water bridges: C:D.215, C:L.218

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

SO4.5: 3 residues within 4Å: Chain A: Y.69, R.183, R.206 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.183, A:R.183, A:R.206 Salt bridges: A:R.183, A:R.206 SO4.8: 4 residues within 4Å: Chain C: K.78, K.85, S.86, K.104 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.86, C:S.86 Water bridges: C:K.78, C:K.78 Salt bridges: C:K.78, C:K.85, C:K.104 SO4.9: 3 residues within 4Å: Chain C: N.131, P.199, K.201 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.131 Salt bridges: C:K.201 SO4.10: 4 residues within 4Å: Chain C: M.38, P.39, E.40, K.67 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.40 Water bridges: C:L.36, C:V.41, C:K.67 Salt bridges: C:K.67

2 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.6: 4 residues within 4Å: Chain A: E.167 Chain B: R.88 Chain C: K.410, L.411 10 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 8 interactions with chain B Water bridges: A:Y.169, B:N.99, B:G.117, B:G.117, B:G.117, B:G.117, B:G.117 Hydrogen bonds: C:K.410, B:R.88, B:R.88 PEO.7: 5 residues within 4Å: Chain B: Y.24, P.28, V.47, G.48, V.51 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.24 Water bridges: B:G.48, B:G.48

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 7 residues within 4Å: Chain C: F.329, Q.342, F.345, N.346, V.347, N.348, G.351 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.347

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 4 residues within 4Å: Chain C: A.105, R.108, N.167, G.168 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.108, C:N.167, C:G.168 Water bridges: C:D.88, C:R.108, C:Q.170

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
Profilin-1: B
Putative Adenylate cyclase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Actin, alpha skeletal muscle, intermediate form

Profilin-1

Putative Adenylate cyclase

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