- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x LAB: LATRUNCULIN B(Non-covalent)
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.2: 24 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: LAB.1, MG.3, MN.4
16 PLIP interactions:16 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
- Salt bridges: A:K.18, A:K.18
- pi-Stacking: A:Y.306
- 3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.3: 2 residues within 4Å:- Ligands: ATP.2, MN.4
No protein-ligand interaction detected (PLIP)MG.8: 6 residues within 4Å:- Chain B: D.215, D.217
- Ligands: 3AT.6, MN.7, MN.9, MG.10
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.215, B:D.217, H2O.2
MG.10: 7 residues within 4Å:- Chain B: D.215, D.217, H.303
- Ligands: 3AT.6, MN.7, MG.8, MN.9
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.215, B:D.215, B:D.217, B:H.303
- 6 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)
MN.4: 2 residues within 4Å:- Ligands: ATP.2, MG.3
No protein-ligand interaction detected (PLIP)MN.7: 6 residues within 4Å:- Chain B: D.215, D.217
- Ligands: 3AT.6, MG.8, MN.9, MG.10
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.215, B:D.217, H2O.2
MN.9: 7 residues within 4Å:- Chain B: D.215, D.217, H.303
- Ligands: 3AT.6, MN.7, MG.8, MG.10
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.215, B:D.215, B:D.217, B:H.303
MN.12: 6 residues within 4Å:- Chain B: E.119
- Ligands: MN.13, AZI.15, AZI.16, AZI.19, CL.22
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.119
MN.13: 7 residues within 4Å:- Chain B: E.119
- Ligands: MN.12, MN.14, AZI.15, AZI.16, AZI.17, AZI.20
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.119
MN.14: 5 residues within 4Å:- Ligands: MN.13, AZI.17, AZI.18, AZI.20, CL.21
No protein-ligand interaction detected (PLIP)- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 3 residues within 4Å:- Chain A: H.73, R.177, D.179
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:H.73, A:R.177
SO4.11: 6 residues within 4Å:- Chain B: S.68, L.69, S.72, Y.75, N.135, E.141
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.72, B:Y.75, B:Y.75, B:N.135
- Water bridges: B:N.135
- 1 x 3AT: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
3AT.6: 21 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: MN.7, MG.8, MN.9, MG.10
22 PLIP interactions:22 interactions with chain B- Hydrophobic interactions: B:L.80
- Hydrogen bonds: B:K.83, B:S.86, B:S.86, B:D.215, B:M.276, B:M.276, B:H.303, B:G.304, B:N.309
- Water bridges: B:R.60, B:K.85, B:K.85
- 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
- 6 x AZI: AZIDE ION(Non-functional Binders)(Non-covalent)
AZI.15: 2 residues within 4Å:- Ligands: MN.12, MN.13
No protein-ligand interaction detected (PLIP)AZI.16: 5 residues within 4Å:- Chain B: E.119
- Ligands: MN.12, MN.13, AZI.19, CL.22
No protein-ligand interaction detected (PLIP)AZI.17: 6 residues within 4Å:- Chain B: E.116, E.119, L.123
- Ligands: MN.13, MN.14, AZI.20
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.116
AZI.18: 3 residues within 4Å:- Ligands: MN.14, AZI.20, CL.21
No protein-ligand interaction detected (PLIP)AZI.19: 3 residues within 4Å:- Ligands: MN.12, AZI.16, CL.22
No protein-ligand interaction detected (PLIP)AZI.20: 5 residues within 4Å:- Ligands: MN.13, MN.14, AZI.17, AZI.18, CL.21
No protein-ligand interaction detected (PLIP)- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 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
CB
D
SMTL ID : 8bo1.2 (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
Actin, alpha skeletal muscle, intermediate form
Putative Adenylate cyclase
Related Entries With Identical Sequence
1h1v.1 | 1j6z.1 | 1kxp.1 | 1lot.1 | 1m8q.1 | 1ma9.1 | 1mvw.1 | 1nwk.1 | 1o18.1 | 1o19.1 | 1o1a.1 | 1o1b.1 | 1o1c.1 | 1o1d.1 | 1o1e.1 | 1o1f.1 | 1o1g.1 | 1qz5.1 | 1qz6.1 | 1rdw.1 | 1rfq.1 | 1s22.1 | 1wua.1 | 1y64.1 | 1yxq.1 | 2a3z.1 | 2a40.1 | 2a40.2 | 2a40.3 | 2a41.1 more...less...2a42.1 | 2a5x.1 | 2asm.1 | 2aso.1 | 2asp.1 | 2d1k.1 | 2ff3.1 | 2ff6.1 | 2fxu.1 | 2hmp.1 | 2pav.1 | 2q0r.1 | 2q0u.1 | 2q1n.1 | 2q1n.2 | 2q31.1 | 2q31.2 | 2q36.1 | 2q97.1 | 2q97.2 | 2vcp.1 | 2vcp.2 | 2y83.1 | 2zwh.1 | 3buz.1 | 3hbt.1 | 3j4k.1 | 3j8a.1 | 3jbi.1 | 3jbj.1 | 3jbk.1 | 3m1f.1 | 3m3n.1 | 3mfp.1 | 3mfp.2 | 3mfp.3 | 3sjh.1 | 3tpq.1 | 3u8x.1 | 3u8x.2 | 3u9d.1 | 3u9d.2 | 3u9z.1 | 3ue5.1 | 3ue5.2 | 3ue5.3 | 4a7f.1 | 4a7h.1 | 4a7l.1 | 4a7n.1 | 4gy2.1 | 4h03.1 | 4h0t.1 | 4h0v.1 | 4h0x.1 | 4h0y.1 | 4k41.1 | 4k42.1 | 4k42.2 | 4k42.3 | 4k42.4 | 4k43.1 | 4k43.2 | 4pl8.1 | 4v0u.6 | 4v0u.7 | 4v0u.8 | 4v0u.9 | 4v0u.10 | 5h53.1 | 5jlf.1 | 5mva.1 | 5mvy.1 | 5onv.1 | 5ooc.1 | 5ood.1 | 5ooe.1 | 5oof.1 | 5yu8.1 | 6c1d.1 | 6c1g.1 | 6c1h.1 | 6d8c.1 | 6djm.1 | 6djn.1 | 6djo.1 | 6fhl.1 | 6fm2.1 | 6kll.1 | 6kln.1 | 6kn7.1 | 6kn8.1 | 6rsw.1 | 6t1y.1 | 6t20.1 | 6t23.1 | 6t24.1 | 6t25.1 | 6upv.1 | 6upw.1 | 6yp9.1 | 7c2f.1 | 7c2f.2 | 7k20.1 | 7k21.1 | 7ko4.1 | 7ko5.1 | 7ko7.1 | 7kon.1 | 7kor.1 | 7nxv.1 | 7nxv.2 | 7nzm.1 | 7t5q.1 | 8a2r.1 | 8a2s.1 | 8a2t.1 | 8a2u.1 | 8a2y.1 | 8a2z.1 | 8bjh.1 | 8bji.1 | 8bjj.1 | 8bo1.1 | 8br0.1 | 8br0.2 | 8br1.1 | 8br1.2 | 8dmx.1 | 8e9b.1 | 8of8.1 | 8ru0.1 | 8rv2.1 | 8syf.1 | 8uee.1 | 9fjo.1