SMTL ID : 6gvr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x NDG- GLA- GLC- RAM- NAG: 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(Non-covalent)(Non-functional Binders)

NDG-GLA-GLC-RAM-NAG.1: 24 residues within 4Å: Chain A: G.101, H.102, Q.132, F.137, P.142, L.172, T.197, W.198, T.201, W.204, N.205, D.229, H.230, S.231, Y.234, N.236, Q.262, H.264, Y.283, V.285, H.287, A.289, E.290 Ligands: NA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.287, A:G.203, A:N.205, A:N.205, A:N.236, A:E.290, A:D.229, A:D.229, A:S.231, A:Q.262, A:H.102, A:Q.132 Hydrophobic interactions: A:A.289, A:E.290, A:T.197, A:D.229, A:F.137, A:P.142 Water bridges: A:T.201, A:H.287, A:G.101, A:H.102 NDG-GLA-GLC-RAM-NAG.9: 24 residues within 4Å: Chain B: G.101, H.102, Q.132, F.137, P.142, L.172, T.197, W.198, T.201, W.204, N.205, D.229, H.230, S.231, Y.234, N.236, Q.262, H.264, Y.283, V.285, H.287, A.289, E.290 Ligands: NA.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.287, B:G.203, B:N.205, B:N.205, B:N.236, B:E.290, B:D.229, B:D.229, B:S.231, B:Q.262, B:H.102, B:Q.132 Hydrophobic interactions: B:A.289, B:E.290, B:T.197, B:D.229, B:F.137, B:P.142 Water bridges: B:T.201, B:H.287, B:G.101, B:H.102 NDG-GLA-GLC-RAM-NAG.17: 24 residues within 4Å: Chain C: G.101, H.102, Q.132, F.137, P.142, L.172, T.197, W.198, T.201, W.204, N.205, D.229, H.230, S.231, Y.234, N.236, Q.262, H.264, Y.283, V.285, H.287, A.289, E.290 Ligands: NA.24 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.287, C:G.203, C:N.205, C:N.205, C:N.236, C:E.290, C:D.229, C:D.229, C:S.231, C:Q.262, C:H.102, C:Q.132 Hydrophobic interactions: C:A.289, C:E.290, C:T.197, C:D.229, C:F.137, C:P.142 Water bridges: C:T.201, C:H.287, C:G.101, C:H.102

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.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.558, A:R.585, A:R.585 Water bridges: A:D.558 TRS.10: 4 residues within 4Å: Chain B: D.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.558, B:R.585, B:R.585 Water bridges: B:D.558 TRS.18: 4 residues within 4Å: Chain C: D.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.558, C:R.585, C:R.585 Water bridges: C:D.558

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

FMT.3: 8 residues within 4Å: Chain A: I.357, G.358, P.359, G.361, A.362, S.363, R.393, A.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.358, A:G.361, A:Q.366 FMT.4: 2 residues within 4Å: Chain A: Y.485, N.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.513, A:N.513 FMT.5: 3 residues within 4Å: Chain A: W.43 Chain C: R.30, D.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.30, C:D.34 FMT.6: 3 residues within 4Å: Chain A: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 FMT.11: 8 residues within 4Å: Chain B: I.357, G.358, P.359, G.361, A.362, S.363, R.393, A.394 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.358, B:G.361, B:Q.366 FMT.12: 2 residues within 4Å: Chain B: Y.485, N.513 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.513, B:N.513 FMT.13: 3 residues within 4Å: Chain A: R.30, D.34 Chain B: W.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.30, A:D.34 FMT.14: 3 residues within 4Å: Chain B: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.528 FMT.19: 8 residues within 4Å: Chain C: I.357, G.358, P.359, G.361, A.362, S.363, R.393, A.394 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.358, C:G.361, C:Q.366 FMT.20: 2 residues within 4Å: Chain C: Y.485, N.513 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.513, C:N.513 FMT.21: 3 residues within 4Å: Chain B: R.30, D.34 Chain C: W.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.30, B:D.34 FMT.22: 3 residues within 4Å: Chain C: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.528

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

NA.7: 3 residues within 4Å: Chain A: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.480, A:Q.482 NA.8: 2 residues within 4Å: Chain A: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.1 No protein-ligand interaction detected (PLIP) NA.15: 3 residues within 4Å: Chain B: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.482, B:Q.482 NA.16: 2 residues within 4Å: Chain B: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.101 NA.23: 3 residues within 4Å: Chain C: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.482, C:Q.482 NA.24: 2 residues within 4Å: Chain C: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.17 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.101

Links

RCSB   PDBe   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