SMTL ID : 6ek7.1

YaxA from Yersinia enterocolitica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MPD.1: 3 residues within 4Å: Chain A: E.130, A.171, L.172 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.130, A:L.134 MPD.2: 8 residues within 4Å: Chain A: L.148, T.152, K.173, L.176, D.177, I.364, N.365, N.366 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.148, A:T.152, A:L.176 Hydrogen bonds: A:D.177, A:D.177, A:N.366 MPD.3: 5 residues within 4Å: Chain A: L.134, I.135, M.138, D.165, V.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.135 Hydrogen bonds: A:D.165, A:D.165 MPD.4: 3 residues within 4Å: Chain A: R.201, N.341, D.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.201, A:N.341, A:D.344 MPD.5: 2 residues within 4Å: Chain A: R.58 Ligands: MPD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.58 MPD.6: 6 residues within 4Å: Chain A: N.123, I.124, T.127, D.178, M.179, D.182 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.124, A:M.179 Hydrogen bonds: A:N.123, A:N.123, A:T.127 MPD.7: 3 residues within 4Å: Chain A: D.116, A.120, H.186 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.116, A:A.120 Hydrogen bonds: A:H.186 MPD.8: 7 residues within 4Å: Chain A: E.219, K.223, Y.226, F.326, S.327, G.330, I.331 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.223, A:Y.226 MPD.9: 3 residues within 4Å: Chain A: V.408, Y.409 Ligands: MPD.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.408, A:Y.409 Hydrogen bonds: A:Y.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brauning, B. et al., Structure and mechanism of the two-component alpha-helical pore-forming toxin YaxAB. Nat Commun (2018)

Release Date

2018-05-16

Peptides

YaxA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YaxA

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