SMTL ID : 2x85.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

NAG-GLA-GLC-RAM-NAG-GLC.1: 32 residues within 4Å: Chain A: G.102, H.103, Q.133, F.138, P.143, L.173, T.198, W.199, T.202, W.205, N.206, D.230, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: NA.3, NA.4, NA.5 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.230, A:H.288, A:S.320, A:S.320, A:P.360, A:N.362, A:R.396, A:T.202, A:H.103 Hydrogen bonds: A:S.320, A:D.321, A:G.359, A:N.362, A:N.206, A:N.206, A:N.237, A:E.291, A:H.103, A:Q.133 Hydrophobic interactions: A:A.290, A:E.291, A:F.138, A:P.143 NAG-GLA-GLC-RAM-NAG-GLC.7: 32 residues within 4Å: Chain B: G.102, H.103, Q.133, F.138, P.143, L.173, T.198, W.199, T.202, W.205, N.206, D.230, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: NA.9, NA.10, NA.11 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.230, B:H.288, B:S.320, B:S.320, B:P.360, B:N.362, B:R.396, B:T.202, B:H.103 Hydrogen bonds: B:S.320, B:D.321, B:G.359, B:N.362, B:N.206, B:N.206, B:N.237, B:E.291, B:H.103, B:Q.133 Hydrophobic interactions: B:A.290, B:E.291, B:F.138, B:P.143 NAG-GLA-GLC-RAM-NAG-GLC.13: 32 residues within 4Å: Chain C: G.102, H.103, Q.133, F.138, P.143, L.173, T.198, W.199, T.202, W.205, N.206, D.230, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, A.290, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: NA.15, NA.16, NA.17 5 PLIP interactions: 5 interactions with chain C Water bridges: C:D.230, C:H.288, C:S.320, C:S.320, C:P.360, C:N.362, C:R.396, C:T.202, C:H.103 Hydrogen bonds: C:S.320, C:D.321, C:G.359, C:N.362, C:N.206, C:N.206, C:N.237, C:E.291, C:H.103, C:Q.133 Hydrophobic interactions: C:A.290, C:E.291, C:F.138, C:P.143

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

NA.2: 3 residues within 4Å: Chain A: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.483, A:Q.485 NA.3: 3 residues within 4Å: Chain A: Y.284 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.1, NAG-GLA-GLC-RAM-NAG-GLC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.284 Water bridges: A:Y.284 NA.4: 2 residues within 4Å: Chain A: G.102 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.102 NA.5: 7 residues within 4Å: Chain A: D.230, H.231, S.232, I.258, C.260, E.263 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.231, A:I.258 Water bridges: A:Y.284, A:Y.284 NA.8: 3 residues within 4Å: Chain B: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.485, B:Q.485 NA.9: 3 residues within 4Å: Chain B: Y.284 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.7, NAG-GLA-GLC-RAM-NAG-GLC.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.284 Water bridges: B:Y.284 NA.10: 2 residues within 4Å: Chain B: G.102 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.102 NA.11: 7 residues within 4Å: Chain B: D.230, H.231, S.232, I.258, C.260, E.263 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.230, B:H.231 Water bridges: B:Y.284, B:Y.284 NA.14: 3 residues within 4Å: Chain C: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.485, C:Q.485 NA.15: 3 residues within 4Å: Chain C: Y.284 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.13, NAG-GLA-GLC-RAM-NAG-GLC.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.284 Water bridges: C:Y.284 NA.16: 2 residues within 4Å: Chain C: G.102 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.102 NA.17: 7 residues within 4Å: Chain C: D.230, H.231, S.232, I.258, C.260, E.263 Ligands: NAG-GLA-GLC-RAM-NAG-GLC.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.231, C:E.263 Water bridges: C:Y.284, C:Y.284

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

TRS.6: 3 residues within 4Å: Chain A: V.459, N.460, Y.488 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.460 Water bridges: C:E.470, C:E.470 TRS.12: 3 residues within 4Å: Chain B: V.459, N.460, Y.488 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.460 Water bridges: A:E.470, A:E.470 TRS.18: 3 residues within 4Å: Chain C: V.459, N.460, Y.488 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.460 Water bridges: B:E.470, B:E.470

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

2011-03-23

Peptides

TAILSPIKE PROTEIN HK620: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

TAILSPIKE PROTEIN HK620

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