SMTL ID : 2x6w.1

Tailspike protein mutant E372Q of E.coli bacteriophage HK620 in complex with hexasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

3 x NDG- GLA- NAG- GLC- GLC- RAM- NAG: alpha-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-GLA-NAG-GLC-GLC-RAM-NAG.1: 31 residues within 4Å: Chain A: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, W.205, N.206, D.230, H.231, S.232, Y.235, N.237, Q.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, D.321, G.359, P.360, D.361, N.362 Ligands: NA.2, NA.3, NA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.288, A:G.204, A:N.206, A:N.206, A:N.237, A:E.291, A:D.230, A:D.230, A:S.232, A:Q.263, A:N.362, A:H.103, A:Q.133 Water bridges: A:D.230, A:N.362, A:Y.284, A:H.288, A:G.102 Hydrophobic interactions: A:A.290, A:E.291, A:T.198, A:D.230, A:F.138 NDG-GLA-NAG-GLC-GLC-RAM-NAG.6: 31 residues within 4Å: Chain B: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, W.205, N.206, D.230, H.231, S.232, Y.235, N.237, Q.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, D.321, G.359, P.360, D.361, N.362 Ligands: NA.7, NA.8, NA.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.288, B:G.204, B:N.206, B:N.206, B:N.237, B:E.291, B:D.230, B:D.230, B:S.232, B:Q.263, B:N.362, B:H.103, B:Q.133 Water bridges: B:D.230, B:N.362, B:Y.284, B:H.288, B:G.102 Hydrophobic interactions: B:A.290, B:E.291, B:T.198, B:D.230, B:F.138 NDG-GLA-NAG-GLC-GLC-RAM-NAG.11: 31 residues within 4Å: Chain C: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, W.205, N.206, D.230, H.231, S.232, Y.235, N.237, Q.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, D.321, G.359, P.360, D.361, N.362 Ligands: NA.12, NA.13, NA.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.288, C:G.204, C:N.206, C:N.206, C:N.237, C:E.291, C:D.230, C:D.230, C:S.232, C:Q.263, C:N.362, C:H.103, C:Q.133 Water bridges: C:D.230, C:N.362, C:Y.284, C:H.288, C:G.102 Hydrophobic interactions: C:A.290, C:E.291, C:T.198, C:D.230, C:F.138

9 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.230 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.1, NDG-GLA-NAG-GLC-GLC-RAM-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230 Water bridges: A:D.230 NA.3: 8 residues within 4Å: Chain A: D.230, H.231, S.232, I.258, C.260, Q.263 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.1, NDG-GLA-NAG-GLC-GLC-RAM-NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.263 Water bridges: A:R.281, A:Y.284, A:Y.284 NA.4: 2 residues within 4Å: Chain A: G.102 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.1 No protein-ligand interaction detected (PLIP) NA.7: 3 residues within 4Å: Chain B: D.230 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.6, NDG-GLA-NAG-GLC-GLC-RAM-NAG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230 Water bridges: B:D.230 NA.8: 8 residues within 4Å: Chain B: D.230, H.231, S.232, I.258, C.260, Q.263 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.6, NDG-GLA-NAG-GLC-GLC-RAM-NAG.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.230 Water bridges: B:R.281, B:Y.284, B:Y.284 NA.9: 2 residues within 4Å: Chain B: G.102 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.102 NA.12: 3 residues within 4Å: Chain C: D.230 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.11, NDG-GLA-NAG-GLC-GLC-RAM-NAG.11 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.230, C:D.230 NA.13: 8 residues within 4Å: Chain C: D.230, H.231, S.232, I.258, C.260, Q.263 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.11, NDG-GLA-NAG-GLC-GLC-RAM-NAG.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.230 Water bridges: C:R.281, C:Y.284, C:Y.284 NA.14: 2 residues within 4Å: Chain C: G.102 Ligands: NDG-GLA-NAG-GLC-GLC-RAM-NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.102

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 3 residues within 4Å: Chain A: V.459, N.460, Y.488 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.460 Water bridges: B:E.470, B:E.470 TRS.10: 3 residues within 4Å: Chain B: V.459, N.460, Y.488 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.460 Water bridges: C:E.470, C:E.470 TRS.15: 3 residues within 4Å: Chain C: V.459, N.460, Y.488 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.470, A:E.470 Hydrogen bonds: C:N.460

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broeker, N.K. et al., Single Amino Acid Exchange in Bacteriophage Hk620 Tailspike Protein Results in Thousand-Fold Increase of its Oligosaccharide Affinity. Glycobiology (2013)

Release Date

2011-03-02

Peptides

TAIL SPIKE PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

TAIL SPIKE PROTEIN

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