SMTL ID : 6g0x.1

TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH PENTASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x NAG- 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-beta-D-glucopyranose(Non-covalent)

NAG-GLA-GLC-RAM-NAG.1: 23 residues within 4Å: Chain A: G.101, H.102, Q.132, F.137, L.172, T.197, W.198, T.201, W.204, N.205, D.229, S.231, Y.234, N.236, E.262, H.264, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: NA.10 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.287, A:T.201, A:G.203, A:G.101, A:H.102 Hydrophobic interactions: A:A.289, A:E.290, A:F.137 Hydrogen bonds: A:N.205, A:N.205, A:N.236, A:E.290, A:H.102, A:Q.132

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

TRS.2: 3 residues within 4Å: Chain A: V.458, N.459, Y.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.459 Water bridges: A:N.459

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

FMT.3: 3 residues within 4Å: Chain A: N.558, L.559, D.560 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.559, A:D.560, A:D.560 FMT.4: 2 residues within 4Å: Chain A: L.559, E.582 No protein-ligand interaction detected (PLIP) FMT.5: 5 residues within 4Å: Chain A: P.56, G.57, Y.87, T.88, Y.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.88 Water bridges: A:G.86 FMT.6: 6 residues within 4Å: Chain A: V.524, N.525, S.539, T.540, D.541, Y.544 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.523, A:N.525, A:T.540, A:T.540, A:D.541 Water bridges: A:N.525, A:N.525 FMT.7: 2 residues within 4Å: Chain A: R.30, D.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.30 Water bridges: A:D.34, A:D.34, A:D.34

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

NA.8: 1 residues within 4Å: Chain A: N.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.407 Water bridges: A:N.407 NA.9: 3 residues within 4Å: Chain A: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.482, A:Q.484 NA.10: 2 residues within 4Å: Chain A: G.101 Ligands: NAG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A: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

2018-04-04

Peptides

Tail spike protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tail spike protein