SMTL ID : 4xr6.1

Tailspike protein double mutant D339A/E372Q of E. coli bacteriophage HK620 in complex with hexasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 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.99, H.100, Q.130, F.135, L.170, T.195, W.196, T.199, W.202, N.203, A.227, H.228, S.229, Y.232, N.234, Q.260, Y.281, V.283, H.285, A.287, E.288, L.315, G.316, D.318, G.356, P.357, D.358, N.359 Ligands: NA.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.285, A:D.318, A:D.318, A:G.356, A:N.359, A:G.201, A:N.203, A:N.203, A:N.234, A:E.288, A:S.229, A:Q.260, A:N.359, A:H.100, A:Q.130 Water bridges: A:S.317, A:S.317, A:P.357, A:N.359, A:T.199, A:S.229, A:H.285, A:G.99 Hydrophobic interactions: A:A.287, A:E.288, A:T.195, A:A.227, A:F.135 NDG-GLA-GLC-RAM-NAG-GLC.10: 29 residues within 4Å: Chain B: G.99, H.100, Q.130, F.135, L.170, T.195, W.196, T.199, W.202, N.203, A.227, H.228, S.229, Y.232, N.234, Q.260, Y.281, V.283, H.285, A.287, E.288, L.315, G.316, D.318, G.356, P.357, D.358, N.359 Ligands: NA.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.285, B:D.318, B:D.318, B:G.356, B:N.359, B:G.201, B:N.203, B:N.203, B:N.234, B:E.288, B:S.229, B:Q.260, B:N.359, B:H.100, B:Q.130 Water bridges: B:S.317, B:S.317, B:P.357, B:N.359, B:T.199, B:S.229, B:H.285, B:G.99 Hydrophobic interactions: B:A.287, B:E.288, B:T.195, B:A.227, B:F.135 NDG-GLA-GLC-RAM-NAG-GLC.19: 29 residues within 4Å: Chain C: G.99, H.100, Q.130, F.135, L.170, T.195, W.196, T.199, W.202, N.203, A.227, H.228, S.229, Y.232, N.234, Q.260, Y.281, V.283, H.285, A.287, E.288, L.315, G.316, D.318, G.356, P.357, D.358, N.359 Ligands: NA.27 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.285, C:D.318, C:D.318, C:G.356, C:N.359, C:G.201, C:N.203, C:N.203, C:N.234, C:E.288, C:S.229, C:Q.260, C:N.359, C:H.100, C:Q.130 Water bridges: C:S.317, C:S.317, C:P.357, C:N.359, C:T.199, C:S.229, C:H.285, C:G.99 Hydrophobic interactions: C:A.287, C:E.288, C:T.195, C:A.227, C:F.135

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

TRS.2: 3 residues within 4Å: Chain A: V.456, N.457, Y.485 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.467, A:N.457 Water bridges: B:E.467 TRS.11: 3 residues within 4Å: Chain B: V.456, N.457, Y.485 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.467, B:N.457 Water bridges: C:E.467 TRS.20: 3 residues within 4Å: Chain C: V.456, N.457, Y.485 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.467, C:N.457 Water bridges: A:E.467

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

FMT.3: 3 residues within 4Å: Chain A: N.556, L.557, D.558 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.557, A:D.558 FMT.4: 6 residues within 4Å: Chain A: V.522, N.523, S.537, T.538, D.539, Y.542 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.521, A:N.523, A:N.523, A:T.538, A:D.539 FMT.5: 3 residues within 4Å: Chain A: R.28, D.32 Chain B: V.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.28 Water bridges: A:D.32 FMT.6: 7 residues within 4Å: Chain A: K.430, S.431, N.432, V.433, Q.463 Chain C: D.429, E.461 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.429, A:N.432 Water bridges: C:S.431, A:I.434 FMT.12: 3 residues within 4Å: Chain B: N.556, L.557, D.558 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.557, B:D.558 FMT.13: 6 residues within 4Å: Chain B: V.522, N.523, S.537, T.538, D.539, Y.542 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.521, B:N.523, B:N.523, B:T.538, B:D.539 FMT.14: 3 residues within 4Å: Chain B: R.28, D.32 Chain C: V.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.28 Water bridges: B:D.32 FMT.15: 7 residues within 4Å: Chain A: D.429, E.461 Chain B: K.430, S.431, N.432, V.433, Q.463 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.429, B:N.432 Water bridges: A:S.431, B:I.434 FMT.21: 3 residues within 4Å: Chain C: N.556, L.557, D.558 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.557, C:D.558 FMT.22: 6 residues within 4Å: Chain C: V.522, N.523, S.537, T.538, D.539, Y.542 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.521, C:N.523, C:N.523, C:T.538, C:D.539 FMT.23: 3 residues within 4Å: Chain A: V.51 Chain C: R.28, D.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.28 Water bridges: C:D.32 FMT.24: 7 residues within 4Å: Chain B: D.429, E.461 Chain C: K.430, S.431, N.432, V.433, Q.463 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.429, C:N.432 Water bridges: B:S.431, C:I.434

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

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:Q.482, A:Q.482 NA.8: 4 residues within 4Å: Chain A: N.405 Chain C: R.370, V.371, T.400 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.405, C:V.371, C:V.371 Water bridges: C:C.399 NA.9: 2 residues within 4Å: Chain A: G.99 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.1 No protein-ligand interaction detected (PLIP) NA.16: 3 residues within 4Å: Chain B: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.480, B:Q.482 NA.17: 4 residues within 4Å: Chain A: R.370, V.371, T.400 Chain B: N.405 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.371, A:V.371, B:N.405 Water bridges: A:C.399 NA.18: 2 residues within 4Å: Chain B: G.99 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.10 No protein-ligand interaction detected (PLIP) NA.25: 3 residues within 4Å: Chain C: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.453, C:Q.482 NA.26: 4 residues within 4Å: Chain B: R.370, V.371, T.400 Chain C: N.405 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:V.371, B:T.400, C:N.405 Water bridges: B:C.399 NA.27: 2 residues within 4Å: Chain C: G.99 Ligands: NDG-GLA-GLC-RAM-NAG-GLC.19 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

2016-01-27

Peptides

Tail spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail spike protein

Related Entries With Identical Sequence