SMTL ID : 4xor.1

Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620 in complex with pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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: 25 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, N.227, H.228, S.229, Y.232, N.234, Q.260, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: FMT.6, NA.9 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.227, A:N.227, A:H.285, A:H.285, A:G.99 Hydrophobic interactions: A:A.287, A:E.288, A:T.195, A:N.227, A:F.135 Hydrogen bonds: A:G.201, A:N.203, A:N.203, A:N.234, A:E.288, A:N.227, A:N.227, A:N.227, A:S.229, A:Q.260, A:N.359, A:H.100, A:Q.130 NDG-GLA-GLC-RAM-NAG.10: 25 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, N.227, H.228, S.229, Y.232, N.234, Q.260, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: FMT.15, NA.18 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.227, B:N.227, B:H.285, B:H.285, B:G.99 Hydrophobic interactions: B:A.287, B:E.288, B:T.195, B:N.227, B:F.135 Hydrogen bonds: B:G.201, B:N.203, B:N.203, B:N.234, B:E.288, B:N.227, B:N.227, B:N.227, B:S.229, B:Q.260, B:N.359, B:H.100, B:Q.130 NDG-GLA-GLC-RAM-NAG.19: 25 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, N.227, H.228, S.229, Y.232, N.234, Q.260, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: FMT.24, NA.27 4 PLIP interactions: 4 interactions with chain C Water bridges: C:N.227, C:N.227, C:H.285, C:H.285, C:G.99 Hydrophobic interactions: C:A.287, C:E.288, C:T.195, C:N.227, C:F.135 Hydrogen bonds: C:G.201, C:N.203, C:N.203, C:N.234, C:E.288, C:N.227, C:N.227, C:N.227, C:S.229, C:Q.260, C:N.359, C:H.100, C:Q.130

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.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.558, A:R.585, A:R.585 Water bridges: A:D.558 TRS.11: 4 residues within 4Å: Chain B: D.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.558, B:R.585, B:R.585 Water bridges: B:D.558 TRS.20: 4 residues within 4Å: Chain C: D.558, I.581, G.582, R.585 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.558, C:R.585, C:R.585 Water bridges: C:D.558

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

FMT.3: 4 residues within 4Å: Chain A: W.41, V.51 Chain C: R.28, D.32 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:W.41, C:D.32 Hydrogen bonds: C:R.28 FMT.4: 3 residues within 4Å: Chain A: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 FMT.5: 3 residues within 4Å: Chain A: Y.485, A.512, N.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.513, A:N.513 FMT.6: 6 residues within 4Å: Chain A: H.100, S.101, P.128, Q.130, L.170 Ligands: NDG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.130 FMT.12: 4 residues within 4Å: Chain A: R.28, D.32 Chain B: W.41, V.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.28 Water bridges: A:D.32, B:W.41 FMT.13: 3 residues within 4Å: Chain B: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.528 FMT.14: 3 residues within 4Å: Chain B: Y.485, A.512, N.513 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.513, B:N.513 FMT.15: 6 residues within 4Å: Chain B: H.100, S.101, P.128, Q.130, L.170 Ligands: NDG-GLA-GLC-RAM-NAG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.130 FMT.21: 4 residues within 4Å: Chain B: R.28, D.32 Chain C: W.41, V.51 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.28 Water bridges: B:D.32, C:W.41 FMT.22: 3 residues within 4Å: Chain C: Y.527, N.528, V.584 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.528 FMT.23: 3 residues within 4Å: Chain C: Y.485, A.512, N.513 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.513, C:N.513 FMT.24: 6 residues within 4Å: Chain C: H.100, S.101, P.128, Q.130, L.170 Ligands: NDG-GLA-GLC-RAM-NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.130

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

NA.7: 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:T.400 Water bridges: C:C.399 NA.8: 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.9: 2 residues within 4Å: Chain A: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.99 NA.16: 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:T.400, B:N.405 Water bridges: A:C.399 NA.17: 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.18: 2 residues within 4Å: Chain B: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.99 NA.25: 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:T.400, B:T.400, C:N.405 Water bridges: B:C.399 NA.26: 3 residues within 4Å: Chain C: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.480, C:Q.482 NA.27: 2 residues within 4Å: Chain C: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.99

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