- 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(Non-covalent)(Non-functional Binders)
- 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.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-covalent)(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:2 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:R.31
- Water bridges: B:D.35, C:W.44
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-covalent)(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:S.481, 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, C:T.401, A:N.406
- Water bridges: C:C.400
NA.8: 2 residues within 4Å:- Chain A: G.102
- Ligands: NDG-GLA-GLC-RAM-NAG-GLC.1
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.102
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:2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:T.401, B:N.406, 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
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.102
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:A.454, 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:V.372, 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 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
AB
AC
A
- 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(Non-covalent)(Non-functional Binders)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)(Non-functional Binders)
- 9 x FMT: FORMIC ACID(Non-covalent)(Non-functional Binders)
- 9 x NA: SODIUM ION(Non-covalent)(Non-functional Binders)
- 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
AB
AC
A