SMTL ID : 6grj.1

Structure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-10-mer

Ligands

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain A: Y.26, S.29, Q.33, Q.260, G.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.33 MPD.2: 3 residues within 4Å: Chain A: K.169, A.172, A.173 No protein-ligand interaction detected (PLIP) MPD.3: 4 residues within 4Å: Chain A: T.320, T.324 Chain J: S.78, K.333 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.78 MPD.8: 4 residues within 4Å: Chain B: S.78, K.333, I.336 Chain E: T.324 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:T.324 Hydrogen bonds: B:S.78 MPD.9: 7 residues within 4Å: Chain B: V.182, G.185 Chain E: G.176, A.177, G.226, A.229 Ligands: MPD.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.182 MPD.12: 1 residues within 4Å: Chain C: A.172 No protein-ligand interaction detected (PLIP) MPD.17: 5 residues within 4Å: Chain B: I.181, L.234 Chain E: K.169, A.173 Ligands: MPD.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:I.181, B:I.181, B:L.234, E:A.173 MPD.18: 6 residues within 4Å: Chain E: Y.26, S.29, V.30, Q.33, Q.260, G.264 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.30, E:Q.33 Hydrogen bonds: E:S.29, E:S.29 MPD.30: 4 residues within 4Å: Chain G: S.29, Q.33, Q.260, G.264 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Q.33 MPD.31: 4 residues within 4Å: Chain F: I.181, L.234 Chain G: A.172, A.173 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:I.181, F:L.234 Hydrogen bonds: G:A.172 MPD.37: 7 residues within 4Å: Chain C: T.259, N.263, K.266 Chain H: P.35, V.36, D.37, I.257 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:I.257 Hydrogen bonds: H:D.37, C:N.263 MPD.43: 6 residues within 4Å: Chain I: Y.26, S.29, V.30, Q.33, Q.260, G.264 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:Q.33, I:Q.260 Hydrogen bonds: I:Y.26, I:Y.26 MPD.44: 3 residues within 4Å: Chain D: L.234 Chain I: A.172, A.173 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.234 MPD.49: 6 residues within 4Å: Chain A: N.263, K.266 Chain J: V.36, D.37, Q.40, I.257 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:N.263, J:D.37 Hydrophobic interactions: J:I.257

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

PO4.4: 7 residues within 4Å: Chain A: S.81, L.326, V.329, T.330, K.333 Chain B: T.324, T.327 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.324, B:T.327, B:T.327, A:S.81, A:T.330 Salt bridges: A:K.333 PO4.32: 5 residues within 4Å: Chain G: F.41, V.159, L.163, K.247 Ligands: CL.33 No protein-ligand interaction detected (PLIP)

27 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: F.41, P.42, N.43 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Q.48, T.49, N.52 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: N.47, Q.50, I.145, N.148, L.149 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: F.41, P.42, N.43 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain D: Q.48, T.49, N.52 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain D: N.47, Q.50, I.145, N.148, L.149 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: N.79 Chain E: N.3, A.4 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain E: Q.242 Chain F: P.42, N.43, E.254 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain E: F.41, P.42, N.43 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain E: Q.48, T.49, N.52 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain E: L.238, R.241 Chain F: V.159, K.247 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain F: N.47, Q.50, I.145, N.148, L.149 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain F: Q.72, N.76 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain G: F.41, P.42, N.43 Ligands: PO4.32 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain G: Q.48, T.49, N.52 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain H: N.47, Q.50, I.145, N.148, L.149 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain H: Q.72, N.76 Ligand excluded by PLIP CL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain H: Q.48, N.52 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain I: F.41, P.42, N.43 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain I: Q.48, T.49, N.52 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain J: N.47, Q.50, I.145, N.148, L.149 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain J: Q.48, T.49, N.52 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain J: N.150, K.266 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain J: Q.72, N.76 Ligand excluded by PLIP

10 x NA: SODIUM ION(Non-functional Binders)

NA.11: 5 residues within 4Å: Chain B: G.54, L.57, A.58, D.138, N.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.54, B:A.58, B:D.138, B:N.141 NA.16: 4 residues within 4Å: Chain C: Q.246 Chain D: N.43, K.152, D.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.43, D:D.156, D:D.156 NA.24: 3 residues within 4Å: Chain E: D.287, T.290, S.291 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.290, E:T.290 NA.25: 6 residues within 4Å: Chain E: S.78, S.81, N.82 Chain F: D.292, S.295, T.321 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.292, F:S.295 NA.26: 4 residues within 4Å: Chain E: Q.16, I.73, N.76, I.77 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.76 NA.29: 3 residues within 4Å: Chain F: H.61, L.131, N.134 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.61, F:N.134 NA.35: 6 residues within 4Å: Chain G: G.12, N.15, Q.16, A.278, Q.281, M.282 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.278, G:Q.281 NA.36: 1 residues within 4Å: Chain G: S.139 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.139 NA.42: 5 residues within 4Å: Chain H: G.54, L.57, A.58, D.138, N.141 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.138, H:D.138, H:N.141 NA.48: 4 residues within 4Å: Chain I: L.238, R.241 Chain J: V.159, K.247 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:L.238, I:R.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilson, J.S. et al., Identification and structural analysis of the tripartite alpha-pore forming toxin of Aeromonas hydrophila. Nat Commun (2019)

Release Date

2019-07-03

Peptides

AhlB: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
J

C
A

D
B

E
C

F
D

G
E

H
F

I
H

J
I

Membrane

We predict this structure to be a membrane protein.
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AhlB