SMTL ID : 7q4t.1

Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x ALA- DGL: ALA-DGL(Non-covalent)

ALA-DGL.1: 5 residues within 4Å: Chain A: Q.141, N.145, Y.148 Ligands: MUB-NAG.2, EDO.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.148 Hydrogen bonds: A:Q.141, A:N.145, A:N.145

1 x MUB- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid(Non-covalent)

MUB-NAG.2: 11 residues within 4Å: Chain A: V.60, H.102, D.106, V.109, R.113, Q.141, V.144, Y.148 Ligands: ALA-DGL.1, ALA-DGL.1, EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.113, A:R.113, A:Q.141, A:H.102, A:D.106 Water bridges: A:R.113

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: M.21, T.24, Q.26, D.27, S.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.150 PEG.4: 7 residues within 4Å: Chain A: D.27, S.30, A.31, D.34, G.152, N.156, V.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.27, A:D.34, A:N.156

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: D.34, K.163, H.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.163, A:K.163 EDO.6: 4 residues within 4Å: Chain A: K.77, D.112, R.113, D.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.77, A:R.113, A:D.114, A:D.114 EDO.7: 3 residues within 4Å: Chain A: W.177, A.178, D.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.178, A:D.195 Water bridges: A:W.177 EDO.8: 3 residues within 4Å: Chain A: H.131, F.161, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 EDO.9: 3 residues within 4Å: Chain A: D.86, L.96, K.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.107, A:K.107 EDO.10: 4 residues within 4Å: Chain A: F.28, K.43, K.47, F.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 EDO.11: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.139 EDO.12: 2 residues within 4Å: Chain A: D.81, I.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.81 EDO.13: 3 residues within 4Å: Chain A: R.76, Q.118, W.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:Q.118, A:W.132 EDO.14: 4 residues within 4Å: Chain A: F.125, Q.126, I.127, Y.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.125 Water bridges: A:M.128 EDO.15: 2 residues within 4Å: Chain A: V.37, D.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.37 Water bridges: A:D.38, A:D.38 EDO.16: 5 residues within 4Å: Chain A: V.48, E.49, S.50, R.51, Y.194 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Ligands: ALA-DGL.1, MUB-NAG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vazquez, R. et al., Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-02-23

Peptides

Endolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Endolysin

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