SMTL ID : 4xm3.1

Tailspike protein mutant E372A of E. coli bacteriophage HK620 in complex with pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 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: 22 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, H.230, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: NA.10 5 PLIP interactions: 5 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:N.361, A:H.102, A:Q.132 Water bridges: A:D.229, A:H.230, A:Y.283, A:H.287, A:G.101, A:H.102 Hydrophobic interactions: A:A.289, A:E.290, A:T.197, A:D.229, A:F.137 NDG-GLA-GLC-RAM-NAG.13: 22 residues within 4Å: Chain B: G.101, H.102, Q.132, F.137, L.172, T.197, W.198, T.201, W.204, N.205, D.229, H.230, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: NA.22 5 PLIP interactions: 5 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:N.361, B:H.102, B:Q.132 Water bridges: B:D.229, B:H.230, B:Y.283, B:H.287, B:G.101, B:H.102 Hydrophobic interactions: B:A.289, B:E.290, B:T.197, B:D.229, B:F.137 NDG-GLA-GLC-RAM-NAG.25: 22 residues within 4Å: Chain C: G.101, H.102, Q.132, F.137, L.172, T.197, W.198, T.201, W.204, N.205, D.229, H.230, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: NA.34 5 PLIP interactions: 5 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:N.361, C:H.102, C:Q.132 Water bridges: C:D.229, C:H.230, C:Y.283, C:H.287, C:G.101, C:H.102 Hydrophobic interactions: C:A.289, C:E.290, C:T.197, C:D.229, C:F.137

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.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.469 Hydrogen bonds: A:N.459 TRS.14: 3 residues within 4Å: Chain B: V.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.459 Water bridges: C:E.469 TRS.26: 3 residues within 4Å: Chain C: V.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:E.469 Hydrogen bonds: C:N.459

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

FMT.3: 3 residues within 4Å: Chain A: N.558, L.559, D.560 Ligand excluded by PLIP FMT.4: 3 residues within 4Å: Chain A: L.559, E.582 Chain C: K.570 Ligand excluded by PLIP FMT.5: 5 residues within 4Å: Chain A: P.56, G.57, Y.87, T.88, Y.90 Ligand excluded by PLIP FMT.6: 5 residues within 4Å: Chain A: N.407, V.435 Chain C: R.372, T.402 Ligands: NA.11 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: V.524, N.525, S.539, T.540, D.541, Y.544 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: R.30, D.34 Chain B: W.43 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: G.358, P.359, R.395 Ligand excluded by PLIP FMT.15: 3 residues within 4Å: Chain B: N.558, L.559, D.560 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain A: K.570 Chain B: L.559, E.582 Ligand excluded by PLIP FMT.17: 5 residues within 4Å: Chain B: P.56, G.57, Y.87, T.88, Y.90 Ligand excluded by PLIP FMT.18: 5 residues within 4Å: Chain A: R.372, T.402 Chain B: N.407, V.435 Ligands: NA.23 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain B: V.524, N.525, S.539, T.540, D.541, Y.544 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain B: R.30, D.34 Chain C: W.43 Ligand excluded by PLIP FMT.21: 3 residues within 4Å: Chain B: G.358, P.359, R.395 Ligand excluded by PLIP FMT.27: 3 residues within 4Å: Chain C: N.558, L.559, D.560 Ligand excluded by PLIP FMT.28: 3 residues within 4Å: Chain B: K.570 Chain C: L.559, E.582 Ligand excluded by PLIP FMT.29: 5 residues within 4Å: Chain C: P.56, G.57, Y.87, T.88, Y.90 Ligand excluded by PLIP FMT.30: 5 residues within 4Å: Chain B: R.372, T.402 Chain C: N.407, V.435 Ligands: NA.35 Ligand excluded by PLIP FMT.31: 6 residues within 4Å: Chain C: V.524, N.525, S.539, T.540, D.541, Y.544 Ligand excluded by PLIP FMT.32: 3 residues within 4Å: Chain A: W.43 Chain C: R.30, D.34 Ligand excluded by PLIP FMT.33: 3 residues within 4Å: Chain C: G.358, P.359, R.395 Ligand excluded by PLIP

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

NA.10: 2 residues within 4Å: Chain A: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101 NA.11: 5 residues within 4Å: Chain A: N.407 Chain C: R.372, V.373, T.402 Ligands: FMT.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.407, C:T.402 Water bridges: C:C.401 NA.12: 3 residues within 4Å: Chain A: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.484, A:Q.484 NA.22: 2 residues within 4Å: Chain B: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.101 NA.23: 5 residues within 4Å: Chain A: R.372, V.373, T.402 Chain B: N.407 Ligands: FMT.18 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.407, A:V.373 Water bridges: A:C.401 NA.24: 3 residues within 4Å: Chain B: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.484, B:Q.484 NA.34: 2 residues within 4Å: Chain C: G.101 Ligands: NDG-GLA-GLC-RAM-NAG.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.101 NA.35: 5 residues within 4Å: Chain B: R.372, V.373, T.402 Chain C: N.407 Ligands: FMT.30 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.407, C:N.407 Water bridges: B:C.401 NA.36: 3 residues within 4Å: Chain C: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.484, C:Q.484

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