SMTL ID : 4yel.1

Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with hexasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 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: 29 residues within 4Å: Chain A: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, G.200, W.201, N.202, A.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.10 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: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:I.254, A:Y.280, A:H.284, A:G.98, A:H.99 Hydrophobic interactions: A:A.286, A:E.287, A:T.194, A:A.226, A:F.134 NDG-GLA-GLC-RAM-NAG-GLC.11: 29 residues within 4Å: Chain B: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, G.200, W.201, N.202, A.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.20 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: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:I.254, B:Y.280, B:H.284, B:G.98, B:H.99 Hydrophobic interactions: B:A.286, B:E.287, B:T.194, B:A.226, B:F.134 NDG-GLA-GLC-RAM-NAG-GLC.21: 29 residues within 4Å: Chain C: G.98, H.99, Q.129, F.134, L.169, T.194, W.195, T.198, G.200, W.201, N.202, A.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.30 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: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:I.254, C:Y.280, C:H.284, C:G.98, C:H.99 Hydrophobic interactions: C:A.286, C:E.287, C:T.194, C:A.226, C:F.134

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

TRS.2: 4 residues within 4Å: Chain A: D.557, I.580, G.581, R.584 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.557, A:R.584, A:R.584 Water bridges: A:D.557 TRS.12: 4 residues within 4Å: Chain B: D.557, I.580, G.581, R.584 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.557, B:R.584, B:R.584 Water bridges: B:D.557 TRS.22: 4 residues within 4Å: Chain C: D.557, I.580, G.581, R.584 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.557, C:R.584, C:R.584 Water bridges: C:D.557

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

FMT.3: 4 residues within 4Å: Chain A: W.40, V.50 Chain C: R.27, D.31 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.27 Water bridges: C:D.31, C:D.31 FMT.4: 2 residues within 4Å: Chain A: Y.484, N.512 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.512, A:N.512 FMT.5: 3 residues within 4Å: Chain A: L.556, E.579 Chain C: K.567 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.567 Water bridges: C:N.569 FMT.6: 6 residues within 4Å: Chain A: V.521, N.522, S.536, T.537, D.538, Y.541 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.520, A:N.522, A:N.522, A:T.537, A:T.537, A:D.538 FMT.7: 5 residues within 4Å: Chain A: P.53, G.54, Y.84, T.85, Y.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.85 FMT.13: 4 residues within 4Å: Chain A: R.27, D.31 Chain B: W.40, V.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.27 Water bridges: A:D.31, A:D.31 FMT.14: 2 residues within 4Å: Chain B: Y.484, N.512 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.512, B:N.512 FMT.15: 3 residues within 4Å: Chain A: K.567 Chain B: L.556, E.579 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.567 Water bridges: A:N.569 FMT.16: 6 residues within 4Å: Chain B: V.521, N.522, S.536, T.537, D.538, Y.541 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.520, B:N.522, B:N.522, B:T.537, B:T.537, B:D.538 FMT.17: 5 residues within 4Å: Chain B: P.53, G.54, Y.84, T.85, Y.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.85 FMT.23: 4 residues within 4Å: Chain B: R.27, D.31 Chain C: W.40, V.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27 Water bridges: B:D.31, B:D.31 FMT.24: 2 residues within 4Å: Chain C: Y.484, N.512 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.512, C:N.512 FMT.25: 3 residues within 4Å: Chain B: K.567 Chain C: L.556, E.579 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.567 Water bridges: B:N.569 FMT.26: 6 residues within 4Å: Chain C: V.521, N.522, S.536, T.537, D.538, Y.541 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.520, C:N.522, C:N.522, C:T.537, C:T.537, C:D.538 FMT.27: 5 residues within 4Å: Chain C: P.53, G.54, Y.84, T.85, Y.87 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.85

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

NA.8: 4 residues within 4Å: Chain A: N.404 Chain C: R.369, V.370, T.399 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.399, C:T.399, A:N.404 Water bridges: C:C.398 NA.9: 3 residues within 4Å: Chain A: A.452, S.479, Q.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.479, A:Q.481 NA.10: 2 residues within 4Å: Chain A: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.1 No protein-ligand interaction detected (PLIP) NA.18: 4 residues within 4Å: Chain A: R.369, V.370, T.399 Chain B: N.404 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.370, A:T.399, B:N.404 Water bridges: A:C.398 NA.19: 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.20: 2 residues within 4Å: Chain B: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.98 NA.28: 4 residues within 4Å: Chain B: R.369, V.370, T.399 Chain C: N.404 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.404, B:T.399, B:T.399 Water bridges: B:C.398 NA.29: 3 residues within 4Å: Chain C: A.452, S.479, Q.481 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.481, C:Q.481 NA.30: 2 residues within 4Å: Chain C: G.98 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.21 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

2016-03-09

Peptides

Tail spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail spike protein