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

Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen octasaccharide fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x RAM- RAM- NAG- RAM- RAM- RAM- NAG- RAM: alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose

RAM-RAM-NAG-RAM-RAM-RAM-NAG-RAM.1: 17 residues within 4Å: Chain A: A.95, R.122, R.149, E.185, T.207, N.232, I.269, Y.292 Chain B: S.138, D.139, T.140, Q.172, Y.174, W.196, Q.217, V.219, L.281 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.95 Hydrogen bonds: A:R.122, A:R.122, A:R.149, A:E.185 RAM-RAM-NAG-RAM-RAM-RAM-NAG-RAM.2: 20 residues within 4Å: Chain B: A.95, R.122, R.149, E.185, T.207, N.232, I.269, Y.292, W.313 Chain C: D.137, S.138, D.139, T.140, I.170, Q.172, Y.174, W.196, Q.217, V.219, L.281 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.207, B:E.185 Hydrophobic interactions: B:A.95 Hydrogen bonds: B:R.122, B:R.122, B:R.149, B:E.185 RAM-RAM-NAG-RAM-RAM-RAM-NAG-RAM.3: 18 residues within 4Å: Chain A: S.138, D.139, T.140, I.170, Q.172, Y.174, W.196, Q.217, V.219, L.281 Chain C: A.95, R.122, R.149, E.185, T.207, I.269, Y.292, W.313 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.149, C:R.149 Hydrophobic interactions: C:A.95 Hydrogen bonds: C:R.122, C:R.122, C:R.149, C:E.185

5 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 3 residues within 4Å: Chain A: D.27, H.45 Chain B: K.33 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.27, A:H.45, H2O.1, H2O.1, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain A: E.286, Q.287 Chain B: E.286, Q.287 Chain C: E.286 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.286, C:E.286, B:E.286, H2O.8, H2O.8, H2O.13 MN.6: 3 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:E.286, C:E.286, B:E.286 MN.9: 4 residues within 4Å: Chain B: Q.15, D.27, H.45 Chain C: K.33 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.27, B:H.45, H2O.13, H2O.13, H2O.13, H2O.14 MN.12: 3 residues within 4Å: Chain A: K.33 Chain C: D.27, H.45 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.27, C:H.45, H2O.1, H2O.1, H2O.1, H2O.22

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

PO4.7: 4 residues within 4Å: Chain A: R.42, D.46 Chain C: L.55, V.59 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:V.59 Water bridges: C:L.55 Salt bridges: A:R.42 PO4.8: 4 residues within 4Å: Chain A: L.55, V.59 Chain B: R.42, D.46 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.59, B:D.46 Salt bridges: B:R.42

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

EDO.10: 4 residues within 4Å: Chain A: K.396 Chain B: S.372, D.395 Ligands: EDO.11 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Water bridges: A:K.396, C:S.372, B:D.395 EDO.11: 4 residues within 4Å: Chain B: I.340, S.342, S.372 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.372 Water bridges: B:S.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, Y. et al., Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions. J.Am.Chem.Soc. (2016)

Release Date

2015-07-15

Peptides

BIFUNCTIONAL TAIL PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BIFUNCTIONAL TAIL PROTEIN

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