SMTL ID : 4xn3.1

Tailspike protein mutant E372A of E. coli bacteriophage HK620 in complex with hexasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x NDG- 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-alpha-D-glucopyranose(Non-covalent)(Non-functional Binders)

NDG-GLA-GLC-RAM-NAG-GLC.1: 28 residues within 4Å: Chain A: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, W.201, N.202, D.226, H.227, S.228, Y.231, N.233, Y.280, V.282, H.284, A.286, E.287, L.314, G.315, D.317, G.355, P.356, D.357, N.358 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.284, A:S.316, A:D.317, A:G.355, A:N.358, A:G.200, A:N.202, A:N.202, A:N.233, A:E.287, A:D.226, A:D.226, A:N.358, A:H.99, A:Q.129 Water bridges: A:S.316, A:S.316, A:P.356, A:N.358, A:R.392, A:H.227, A:Y.280, A:H.284, A:G.98, A:H.99 Hydrophobic interactions: A:A.286, A:E.287, A:T.194, A:D.226, A:F.134 NDG-GLA-GLC-RAM-NAG-GLC.8: 28 residues within 4Å: Chain B: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, W.201, N.202, D.226, H.227, S.228, Y.231, N.233, Y.280, V.282, H.284, A.286, E.287, L.314, G.315, D.317, G.355, P.356, D.357, N.358 Ligands: NA.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.284, B:S.316, B:D.317, B:G.355, B:N.358, B:G.200, B:N.202, B:N.202, B:N.233, B:E.287, B:D.226, B:D.226, B:N.358, B:H.99, B:Q.129 Water bridges: B:S.316, B:S.316, B:P.356, B:N.358, B:R.392, B:H.227, B:Y.280, B:H.284, B:G.98, B:H.99 Hydrophobic interactions: B:A.286, B:E.287, B:T.194, B:D.226, B:F.134 NDG-GLA-GLC-RAM-NAG-GLC.15: 28 residues within 4Å: Chain C: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, W.201, N.202, D.226, H.227, S.228, Y.231, N.233, Y.280, V.282, H.284, A.286, E.287, L.314, G.315, D.317, G.355, P.356, D.357, N.358 Ligands: NA.21 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.284, C:S.316, C:D.317, C:G.355, C:N.358, C:G.200, C:N.202, C:N.202, C:N.233, C:E.287, C:D.226, C:D.226, C:N.358, C:H.99, C:Q.129 Water bridges: C:S.316, C:S.316, C:P.356, C:N.358, C:R.392, C:H.227, C:Y.280, C:H.284, C:G.98, C:H.99 Hydrophobic interactions: C:A.286, C:E.287, C:T.194, C:D.226, C:F.134

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

TRS.2: 3 residues within 4Å: Chain A: V.455, N.456, Y.484 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:E.466, B:E.466 Hydrogen bonds: A:N.456 TRS.9: 3 residues within 4Å: Chain B: V.455, N.456, Y.484 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.456 Water bridges: C:E.466, C:E.466 TRS.16: 3 residues within 4Å: Chain C: V.455, N.456, Y.484 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.466, A:E.466 Hydrogen bonds: C:N.456

6 x FMT: FORMIC ACID(Non-covalent)(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: N.555, L.556, D.557 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.556, A:D.557, A:D.557 FMT.4: 3 residues within 4Å: Chain A: R.27, D.31 Chain B: V.50 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.27 Water bridges: A:D.31, A:D.31, A:D.31 FMT.10: 3 residues within 4Å: Chain B: N.555, L.556, D.557 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.556, B:D.557, B:D.557 FMT.11: 3 residues within 4Å: Chain B: R.27, D.31 Chain C: V.50 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.27 Water bridges: B:D.31, B:D.31, B:D.31 FMT.17: 3 residues within 4Å: Chain C: N.555, L.556, D.557 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.556, C:D.557, C:D.557 FMT.18: 3 residues within 4Å: Chain A: V.50 Chain C: R.27, D.31 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.27 Water bridges: C:D.31, C:D.31, C:D.31

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

NA.5: 3 residues within 4Å: Chain A: A.452, S.479, Q.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.481, A:Q.481 NA.6: 4 residues within 4Å: Chain A: N.404 Chain C: R.369, V.370, T.399 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.399, C:T.399, A:N.404, A:N.404 Water bridges: C:C.398 NA.7: 2 residues within 4Å: Chain A: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.1 No protein-ligand interaction detected (PLIP) NA.12: 3 residues within 4Å: Chain B: A.452, S.479, Q.481 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.479, B:Q.481 NA.13: 4 residues within 4Å: Chain A: R.369, V.370, T.399 Chain B: N.404 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.370, A:T.399, A:T.399, B:N.404 Water bridges: A:C.398 NA.14: 2 residues within 4Å: Chain B: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.8 No protein-ligand interaction detected (PLIP) NA.19: 3 residues within 4Å: Chain C: A.452, S.479, Q.481 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.479, C:Q.481 NA.20: 4 residues within 4Å: Chain B: R.369, V.370, T.399 Chain C: N.404 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.399, B:T.399, B:T.399, C:N.404 Water bridges: B:C.398 NA.21: 2 residues within 4Å: Chain C: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gohlke, U. et al., Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein. to be published

Release Date

2016-01-27

Peptides

Tail spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail spike protein