SMTL ID : 4ok7.1 (3 other biounits)

Structure of bacteriophage SPN1S endolysin from Salmonella typhimurium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: N.76, Y.77, S.78, G.81, R.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.76, A:S.78 Salt bridges: A:R.101 SO4.2: 3 residues within 4Å: Chain A: Q.170, D.171 Chain B: K.189 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.171 Water bridges: A:R.34, A:A.169, A:E.172 Salt bridges: B:K.189 SO4.3: 1 residues within 4Å: Chain A: K.158 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.158 SO4.4: 1 residues within 4Å: Chain A: K.189 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.189 SO4.7: 3 residues within 4Å: Chain B: H.3, S.5, G.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.3 SO4.8: 5 residues within 4Å: Chain B: N.76, Y.77, S.78, G.81, R.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.78 Salt bridges: B:R.101 SO4.9: 3 residues within 4Å: Chain B: Q.170, D.171 Chain C: K.189 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.171 Water bridges: B:R.34, B:E.172 Salt bridges: C:K.189 SO4.10: 2 residues within 4Å: Chain B: R.124, M.125 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.125 Water bridges: B:G.126, B:G.126, B:N.148 SO4.11: 1 residues within 4Å: Chain B: N.8 No protein-ligand interaction detected (PLIP) SO4.14: 8 residues within 4Å: Chain A: H.3, S.5, G.6 Chain C: F.85, A.88, R.90, Y.121, R.124 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.6 Salt bridges: A:H.3, C:R.90, C:R.124 SO4.15: 3 residues within 4Å: Chain C: H.3, S.5, G.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.6 Salt bridges: C:H.3 SO4.16: 6 residues within 4Å: Chain A: H.1 Chain C: N.76, Y.77, S.78, G.81, R.101 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.78, C:S.78 Salt bridges: C:R.101, A:H.1 SO4.17: 4 residues within 4Å: Chain C: D.193, L.194, V.195, R.196 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.193, C:D.193, C:V.195, C:R.196 Salt bridges: C:R.196 SO4.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.12, G.13, H.14 Chain B: K.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.14, A:H.14 Water bridges: A:N.8, A:Q.12 GOL.6: 4 residues within 4Å: Chain A: S.4, S.5 Chain C: N.202, N.206 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.202, C:N.206, A:S.5 Water bridges: C:N.202 GOL.12: 4 residues within 4Å: Chain B: Q.12, G.13, H.14 Chain C: K.158 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.13, B:H.14, C:K.158, C:K.158 Water bridges: B:N.8, B:Q.12, B:Q.12, B:Q.12, C:K.158, C:K.158 GOL.13: 2 residues within 4Å: Chain B: S.4, S.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y. et al., Structure of bacteriophage SPN1S endolysin reveals an unusual two-module fold for the peptidoglycan lytic and binding activity. Mol.Microbiol. (2014)

Release Date

2014-03-19

Peptides

Endolysin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Endolysin

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