SMTL ID : 4xmy.1

Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

3 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)(Non-functional Binders)

NAG-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, A.229, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: FMT.6, NA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.287, A:N.205, A:N.205, A:N.236, A:E.290, A:H.102, A:Q.132 Water bridges: A:N.361, A:H.102 Hydrophobic interactions: A:A.289, A:E.290, A:F.137 NAG-GLA-GLC-RAM-NAG.10: 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, A.229, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: FMT.15, NA.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.287, B:N.205, B:N.205, B:N.236, B:E.290, B:H.102, B:Q.132 Water bridges: B:N.361, B:H.102 Hydrophobic interactions: B:A.289, B:E.290, B:F.137 NAG-GLA-GLC-RAM-NAG.19: 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, A.229, S.231, Y.234, N.236, Y.283, V.285, H.287, A.289, E.290, N.361 Ligands: FMT.24, NA.26 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.287, C:N.205, C:N.205, C:N.236, C:E.290, C:H.102, C:Q.132 Water bridges: C:N.361, C:H.102 Hydrophobic interactions: C:A.289, C:E.290, 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 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.459 Water bridges: B:E.469, B:E.469 TRS.11: 3 residues within 4Å: Chain B: V.458, N.459, Y.487 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:E.469, C:E.469 Hydrogen bonds: B:N.459 TRS.20: 3 residues within 4Å: Chain C: V.458, N.459, Y.487 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.469, A:E.469 Hydrogen bonds: C:N.459

15 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: 3 residues within 4Å: Chain A: L.559, E.582 Chain C: K.570 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.570 FMT.5: 3 residues within 4Å: Chain A: R.30, D.34 Chain B: W.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.30 Water bridges: A:D.34, A:D.34 FMT.6: 7 residues within 4Å: Chain A: H.230, I.257, A.258, C.259, R.280, Y.283 Ligands: NAG-GLA-GLC-RAM-NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.280, A:Y.283 Water bridges: A:H.230, A:H.230 FMT.7: 7 residues within 4Å: Chain A: K.432, S.433, N.434, V.435, Q.465 Chain C: D.431, E.463 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:I.436, C:S.433 Hydrogen bonds: C:D.431, C:D.431 FMT.12: 3 residues within 4Å: Chain B: N.558, L.559, D.560 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.559, B:D.560, B:D.560 FMT.13: 3 residues within 4Å: Chain A: K.570 Chain B: L.559, E.582 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.570 FMT.14: 3 residues within 4Å: Chain B: R.30, D.34 Chain C: W.43 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.30 Water bridges: B:D.34, B:D.34 FMT.15: 7 residues within 4Å: Chain B: H.230, I.257, A.258, C.259, R.280, Y.283 Ligands: NAG-GLA-GLC-RAM-NAG.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.280, B:Y.283 Water bridges: B:H.230, B:H.230 FMT.16: 7 residues within 4Å: Chain A: D.431, E.463 Chain B: K.432, S.433, N.434, V.435, Q.465 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:I.436, A:S.433 Hydrogen bonds: A:D.431, A:D.431 FMT.21: 3 residues within 4Å: Chain C: N.558, L.559, D.560 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.559, C:D.560, C:D.560 FMT.22: 3 residues within 4Å: Chain B: K.570 Chain C: L.559, E.582 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.570 FMT.23: 3 residues within 4Å: Chain A: W.43 Chain C: R.30, D.34 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.30 Water bridges: C:D.34, C:D.34 FMT.24: 7 residues within 4Å: Chain C: H.230, I.257, A.258, C.259, R.280, Y.283 Ligands: NAG-GLA-GLC-RAM-NAG.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.280, C:Y.283 Water bridges: C:H.230, C:H.230 FMT.25: 7 residues within 4Å: Chain B: D.431, E.463 Chain C: K.432, S.433, N.434, V.435, Q.465 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.431, B:D.431 Water bridges: B:S.433, C:I.436

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

NA.8: 2 residues within 4Å: Chain A: G.101 Ligands: NAG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.101 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.17: 2 residues within 4Å: Chain B: G.101 Ligands: NAG-GLA-GLC-RAM-NAG.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.101 NA.18: 3 residues within 4Å: Chain B: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.482, B:Q.484 NA.26: 2 residues within 4Å: Chain C: G.101 Ligands: NAG-GLA-GLC-RAM-NAG.19 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.101 NA.27: 3 residues within 4Å: Chain C: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.482, 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

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