SMTL ID : 4l92.1 (1 other biounit)

Structure of the RBP from lactococcal phage 1358 in complex with 2 GlcNAc molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 9 residues within 4Å: Chain A: R.237, F.240, N.244, N.289, S.291, A.292, N.341, F.343 Ligands: NAG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.292 Hydrogen bonds: A:R.237, A:R.237, A:N.244, A:N.289, A:S.291, A:S.291, A:S.291, A:N.341 Water bridges: A:S.291, A:A.292 NDG.6: 9 residues within 4Å: Chain B: R.237, F.240, N.244, N.289, S.291, A.292, N.341, F.343 Ligands: NAG.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.292 Hydrogen bonds: B:R.237, B:R.237, B:N.244, B:N.289, B:S.291, B:S.291, B:S.291, B:N.341 Water bridges: B:S.291, B:A.292 NDG.11: 9 residues within 4Å: Chain C: R.237, F.240, N.244, N.289, S.291, A.292, N.341, F.343 Ligands: NAG.12 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.292 Hydrogen bonds: C:R.237, C:R.237, C:N.244, C:N.289, C:S.291, C:S.291, C:S.291, C:N.341 Water bridges: C:S.291, C:A.292

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 8 residues within 4Å: Chain A: V.200, Q.201, S.202, K.239, F.240, D.243, Q.345 Ligands: NDG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.202, A:K.239, A:D.243, A:Q.345 Water bridges: A:V.200, A:S.202, A:S.202, A:S.202, A:S.202, A:S.202, A:D.243, A:N.244 NAG.7: 8 residues within 4Å: Chain B: V.200, Q.201, S.202, K.239, F.240, D.243, Q.345 Ligands: NDG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.202, B:K.239, B:Q.345 Water bridges: B:V.200, B:S.202, B:S.202, B:S.202, B:S.202, B:S.202, B:D.243, B:N.244 NAG.12: 8 residues within 4Å: Chain C: V.200, Q.201, S.202, K.239, F.240, D.243, Q.345 Ligands: NDG.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.202, C:K.239, C:D.243, C:Q.345 Water bridges: C:V.200, C:S.202, C:S.202, C:S.202, C:S.202, C:S.202, C:D.243, C:N.244

9 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: R.254, E.377 Chain B: R.254, E.377 Chain C: R.254, E.377 Ligands: ZN.8, ZN.13 No protein-ligand interaction detected (PLIP) ZN.4: 3 residues within 4Å: Chain A: D.133, H.303, K.338 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.133, A:H.303, H2O.2, H2O.16 ZN.5: 3 residues within 4Å: Chain A: E.16, S.20, H.137 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.16, A:S.20 ZN.8: 8 residues within 4Å: Chain A: R.254, E.377 Chain B: R.254, E.377 Chain C: R.254, E.377 Ligands: ZN.3, ZN.13 No protein-ligand interaction detected (PLIP) ZN.9: 3 residues within 4Å: Chain B: D.133, H.303, K.338 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.133, B:H.303, H2O.18, H2O.33 ZN.10: 3 residues within 4Å: Chain B: E.16, S.20, H.137 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.16, B:S.20 ZN.13: 8 residues within 4Å: Chain A: R.254, E.377 Chain B: R.254, E.377 Chain C: R.254, E.377 Ligands: ZN.3, ZN.8 No protein-ligand interaction detected (PLIP) ZN.14: 3 residues within 4Å: Chain C: D.133, H.303, K.338 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.133, C:H.303, H2O.35, H2O.49 ZN.15: 3 residues within 4Å: Chain C: E.16, S.20, H.137 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.16, C:S.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farenc, C. et al., A Virulent Siphophage CyoEM Structure and Host Recognition and Infection Mechanism. To be Published

Release Date

2014-04-30

Peptides

Receptor Binding Protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Receptor Binding Protein

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