SMTL ID : 7p1g.1

Structure of the P. aeruginosa ExoY-F-actin complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

Ligands

5 x TRP- EEP- ALA- DTH- CYS- HYP- ALA: Phalloidin(Non-covalent)

TRP-EEP-ALA-DTH-CYS-HYP-ALA.1: 17 residues within 4Å: Chain B: E.74, H.75, I.77, T.79, L.112, N.113, P.114, R.179, D.181 Chain F: G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain H: I.289 16 PLIP interactions: 9 interactions with chain F, 2 interactions with chain H, 5 interactions with chain B Hydrophobic interactions: F:Y.200, F:Y.200, F:F.202, F:L.244, H:I.289, B:E.74, B:I.77, B:T.79, B:P.114 Hydrogen bonds: F:G.199, F:G.199, F:G.199, F:S.201, F:S.201, H:R.292, B:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.2: 10 residues within 4Å: Chain D: E.74, H.75, I.77, T.79, L.112, N.113, P.114, R.179, D.181 Chain F: I.289 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:E.74, D:I.77, D:T.79, D:P.114, F:I.289 Hydrogen bonds: D:E.74, F:R.292 TRP-EEP-ALA-DTH-CYS-HYP-ALA.3: 18 residues within 4Å: Chain B: I.289, R.292 Chain D: G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain F: E.74, H.75, I.77, T.79, L.112, N.113, P.114, R.179, D.181 15 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B, 5 interactions with chain F Hydrophobic interactions: D:Y.200, D:Y.200, D:F.202, D:L.244, B:I.289, F:E.74, F:I.77, F:T.79, F:P.114 Hydrogen bonds: D:G.199, D:G.199, D:G.199, D:S.201, B:R.292, F:E.74 TRP-EEP-ALA-DTH-CYS-HYP-ALA.4: 18 residues within 4Å: Chain B: G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain H: E.74, H.75, I.77, T.79, L.112, N.113, P.114, R.179, D.181 Chain J: I.289, R.292 15 PLIP interactions: 2 interactions with chain J, 5 interactions with chain H, 8 interactions with chain B Hydrophobic interactions: J:I.289, H:E.74, H:I.77, H:T.79, H:P.114, B:Y.200, B:Y.200, B:F.202, B:L.244 Hydrogen bonds: J:R.292, H:E.74, B:G.199, B:G.199, B:G.199, B:S.201 TRP-EEP-ALA-DTH-CYS-HYP-ALA.5: 16 residues within 4Å: Chain H: G.199, Y.200, S.201, F.202, E.207, L.244, Q.248 Chain J: E.74, H.75, I.77, T.79, L.112, N.113, P.114, R.179, D.181 14 PLIP interactions: 5 interactions with chain J, 9 interactions with chain H Hydrophobic interactions: J:E.74, J:I.77, J:T.79, J:P.114, H:Y.200, H:Y.200, H:F.202, H:L.244 Hydrogen bonds: J:E.74, H:G.199, H:G.199, H:G.199, H:S.201, H:S.201

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

MG.6: 5 residues within 4Å: Chain A: G.477, D.607, D.609, H.686 Ligands: GH3.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.607, A:D.607, A:H.686 MG.8: 2 residues within 4Å: Ligands: ADP.9, PO4.10 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain C: G.477, D.607, D.609, H.686 Ligands: GH3.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.607, C:D.607, C:H.686 MG.13: 2 residues within 4Å: Ligands: ADP.14, PO4.15 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain E: G.477, D.607, D.609, H.686 Ligands: GH3.17 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.607, E:D.607, E:H.686 MG.18: 2 residues within 4Å: Ligands: ADP.19, PO4.20 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain G: G.477, D.607, D.609, H.686 Ligands: GH3.22 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.607, G:D.607, G:H.686 MG.23: 2 residues within 4Å: Ligands: ADP.24, PO4.25 No protein-ligand interaction detected (PLIP) MG.26: 5 residues within 4Å: Chain I: G.477, D.607, D.609, H.686 Ligands: GH3.27 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.607, I:D.607, I:H.686 MG.28: 2 residues within 4Å: Ligands: ADP.29, PO4.30 No protein-ligand interaction detected (PLIP)

5 x GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GH3.7: 11 residues within 4Å: Chain A: R.459, K.476, F.478, K.483, S.484, E.653, H.686, S.687, N.692, P.693 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.482, A:S.484, A:S.484, A:H.686, A:S.687 Salt bridges: A:R.459, A:K.476, A:K.476, A:K.476, A:K.483 pi-Stacking: A:F.478, A:F.478 GH3.12: 11 residues within 4Å: Chain C: R.459, K.476, F.478, K.483, S.484, E.653, H.686, S.687, N.692, P.693 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.482, C:S.484, C:S.484, C:H.686, C:S.687 Salt bridges: C:R.459, C:K.476, C:K.476, C:K.476, C:K.483 pi-Stacking: C:F.478, C:F.478 GH3.17: 11 residues within 4Å: Chain E: R.459, K.476, F.478, K.483, S.484, E.653, H.686, S.687, N.692, P.693 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.482, E:S.484, E:S.484, E:H.686, E:S.687 Salt bridges: E:R.459, E:K.476, E:K.476, E:K.476, E:K.483 pi-Stacking: E:F.478, E:F.478 GH3.22: 11 residues within 4Å: Chain G: R.459, K.476, F.478, K.483, S.484, E.653, H.686, S.687, N.692, P.693 Ligands: MG.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.482, G:S.484, G:S.484, G:H.686, G:S.687 Salt bridges: G:R.459, G:K.476, G:K.476, G:K.476, G:K.483 pi-Stacking: G:F.478, G:F.478 GH3.27: 11 residues within 4Å: Chain I: R.459, K.476, F.478, K.483, S.484, E.653, H.686, S.687, N.692, P.693 Ligands: MG.26 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.482, I:S.484, I:S.484, I:H.686, I:S.687 Salt bridges: I:R.459, I:K.476, I:K.476, I:K.476, I:K.483 pi-Stacking: I:F.478, I:F.478

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

ADP.9: 19 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8, PO4.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.17, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:E.216, B:G.304, B:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.14: 19 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.13, PO4.15 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.17, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:E.216, D:G.304, D:K.338 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.19: 19 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.18, PO4.20 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.17, F:L.18, F:D.159, F:D.159, F:D.159, F:K.215, F:E.216, F:G.304, F:K.338 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.24: 19 residues within 4Å: Chain H: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.23, PO4.25 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.17, H:L.18, H:D.159, H:D.159, H:D.159, H:K.215, H:E.216, H:G.304, H:K.338 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308 ADP.29: 19 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.28, PO4.30 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.17, J:L.18, J:D.159, J:D.159, J:D.159, J:K.215, J:E.216, J:G.304, J:K.338 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 8 residues within 4Å: Chain B: S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: MG.8, ADP.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:S.16, B:S.16, B:Q.139, B:D.159, B:G.160, B:V.161 PO4.15: 8 residues within 4Å: Chain D: S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: MG.13, ADP.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.16, D:S.16, D:S.16, D:Q.139, D:D.159, D:G.160, D:V.161 PO4.20: 8 residues within 4Å: Chain F: S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: MG.18, ADP.19 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.16, F:S.16, F:S.16, F:Q.139, F:D.159, F:G.160, F:V.161 PO4.25: 8 residues within 4Å: Chain H: S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: MG.23, ADP.24 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:S.16, H:S.16, H:S.16, H:Q.139, H:D.159, H:G.160, H:V.161 PO4.30: 8 residues within 4Å: Chain J: S.16, Q.139, G.158, D.159, G.160, V.161 Ligands: MG.28, ADP.29 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:S.16, J:S.16, J:S.16, J:Q.139, J:D.159, J:G.160, J:V.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Belyy, A. et al., Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens. Nat Commun (2021)

Release Date

2021-11-17

Peptides

Maltose/maltodextrin-binding periplasmic protein,Adenylate cyclase ExoY: ACEGI
Actin, alpha skeletal muscle: BDFHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

C
K

E
L

G
N

I
O

B
C

D
A

F
B

H
D

J
E

Maltose/maltodextrin-binding periplasmic protein,Adenylate cyclase ExoY

Actin, alpha skeletal muscle

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