SMTL ID : 6gvp.1

TAILSPIKE PROTEIN MUTANT E372Q (DELTA N471/S472) OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 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

NDG-GLA-GLC-RAM-NAG-GLC.1: 30 residues within 4Å: Chain A: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, D.230, S.232, Y.235, N.237, Q.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, Q.367 Ligands: NA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.288, A:S.320, A:D.321, A:G.359, 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:H.103, A:Q.133 Water bridges: A:D.230, A:D.230, A:S.320, A:S.320, A:P.360, 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-GLC-RAM-NAG-GLC.9: 30 residues within 4Å: Chain B: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, D.230, S.232, Y.235, N.237, Q.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, Q.367 Ligands: NA.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.288, B:S.320, B:D.321, B:G.359, 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:H.103, B:Q.133 Water bridges: B:D.230, B:D.230, B:S.320, B:S.320, B:P.360, 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-GLC-RAM-NAG-GLC.17: 30 residues within 4Å: Chain C: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, D.230, S.232, Y.235, N.237, Q.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, Q.367 Ligands: NA.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.288, C:S.320, C:D.321, C:G.359, 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:H.103, C:Q.133 Water bridges: C:D.230, C:D.230, C:S.320, C:S.320, C:P.360, 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

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

TRS.2: 4 residues within 4Å: Chain A: D.559, I.582, G.583, R.586 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.559, A:R.586, A:R.586 Water bridges: A:D.559 TRS.10: 4 residues within 4Å: Chain B: D.559, I.582, G.583, R.586 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.559, B:R.586, B:R.586 Water bridges: B:D.559 TRS.18: 4 residues within 4Å: Chain C: D.559, I.582, G.583, R.586 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.559, C:R.586, C:R.586 Water bridges: C:D.559

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: Y.486, A.513, N.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.514, A:N.514 FMT.4: 4 residues within 4Å: Chain A: W.44, V.54 Chain C: R.31, D.35 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.31 Water bridges: C:D.35, A:W.44 FMT.5: 2 residues within 4Å: Chain A: Y.528, N.529 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.529 FMT.11: 3 residues within 4Å: Chain B: Y.486, A.513, N.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.514, B:N.514 FMT.12: 4 residues within 4Å: Chain A: R.31, D.35 Chain B: W.44, V.54 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.31 Water bridges: A:D.35, B:W.44 FMT.13: 2 residues within 4Å: Chain B: Y.528, N.529 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.529 FMT.19: 3 residues within 4Å: Chain C: Y.486, A.513, N.514 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.514, C:N.514 FMT.20: 4 residues within 4Å: Chain B: R.31, D.35 Chain C: W.44, V.54 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:W.44, B:D.35 Hydrogen bonds: B:R.31 FMT.21: 2 residues within 4Å: Chain C: Y.528, N.529 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.529

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

NA.6: 3 residues within 4Å: Chain A: A.454, S.481, Q.483 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.483, A:Q.483 NA.7: 4 residues within 4Å: Chain A: N.406 Chain C: R.371, V.372, T.401 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.401, A:N.406 Water bridges: C:C.400, C:C.400 NA.8: 2 residues within 4Å: Chain A: G.102 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.1 No protein-ligand interaction detected (PLIP) NA.14: 3 residues within 4Å: Chain B: A.454, S.481, Q.483 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.483, B:Q.483 NA.15: 4 residues within 4Å: Chain A: R.371, V.372, T.401 Chain B: N.406 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.372, A:T.401, B:N.406 Water bridges: A:C.400 NA.16: 2 residues within 4Å: Chain B: G.102 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.9 No protein-ligand interaction detected (PLIP) NA.22: 3 residues within 4Å: Chain C: A.454, S.481, Q.483 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.481, C:Q.483 NA.23: 4 residues within 4Å: Chain B: R.371, V.372, T.401 Chain C: N.406 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.401, B:T.401, C:N.406 Water bridges: B:C.400 NA.24: 2 residues within 4Å: Chain C: G.102 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunstmann, S. et al., Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. J. Am. Chem. Soc. (2018)

Release Date

2018-07-11

Peptides

Tail spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail spike protein