SMTL ID : 4yej.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 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: 24 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, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.285, A:S.229, A:Y.281, A:H.285, A:G.99, A:H.100 Hydrophobic interactions: A:A.287, A:E.288, A:T.195, A:A.227, A:F.135 Hydrogen bonds: 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 NDG-GLA-GLC-RAM-NAG.9: 24 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, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: NA.15 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.285, B:S.229, B:Y.281, B:H.285, B:G.99, B:H.100 Hydrophobic interactions: B:A.287, B:E.288, B:T.195, B:A.227, B:F.135 Hydrogen bonds: 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 NDG-GLA-GLC-RAM-NAG.17: 24 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, H.262, Y.281, V.283, H.285, A.287, E.288, N.359 Ligands: NA.23 5 PLIP interactions: 5 interactions with chain C Water bridges: C:H.285, C:S.229, C:Y.281, C:H.285, C:G.99, C:H.100 Hydrophobic interactions: C:A.287, C:E.288, C:T.195, C:A.227, C:F.135 Hydrogen bonds: 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

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 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.467 Hydrogen bonds: A:N.457 TRS.10: 3 residues within 4Å: Chain B: V.456, N.457, Y.485 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.457 Water bridges: C:E.467 TRS.18: 3 residues within 4Å: Chain C: V.456, N.457, Y.485 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:E.467 Hydrogen bonds: C:N.457

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

FMT.3: 3 residues within 4Å: Chain A: N.556, L.557, D.558 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.557, A:D.558, A:D.558 FMT.4: 4 residues within 4Å: Chain A: R.28, D.32 Chain B: W.41, V.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.28 Water bridges: A:D.32, A:D.32, A:D.32 FMT.5: 5 residues within 4Å: Chain A: G.531, Y.578 Chain C: Y.527, T.529, P.534 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.578 Water bridges: A:Q.530, A:Q.530, A:A.532, A:A.532, A:Y.578 FMT.11: 3 residues within 4Å: Chain B: N.556, L.557, D.558 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.557, B:D.558, B:D.558 FMT.12: 4 residues within 4Å: Chain B: R.28, D.32 Chain C: W.41, V.51 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.28 Water bridges: B:D.32, B:D.32, B:D.32 FMT.13: 5 residues within 4Å: Chain A: Y.527, T.529, P.534 Chain B: G.531, Y.578 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.578 Water bridges: B:Q.530, B:Q.530, B:A.532, B:A.532, B:Y.578 FMT.19: 3 residues within 4Å: Chain C: N.556, L.557, D.558 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.557, C:D.558, C:D.558 FMT.20: 4 residues within 4Å: Chain A: W.41, V.51 Chain C: R.28, D.32 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.28 Water bridges: C:D.32, C:D.32, C:D.32 FMT.21: 5 residues within 4Å: Chain B: Y.527, T.529, P.534 Chain C: G.531, Y.578 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.578 Water bridges: C:Q.530, C:Q.530, C:A.532, C:A.532, C:Y.578

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

NA.6: 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.7: 2 residues within 4Å: Chain A: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.1 No protein-ligand interaction detected (PLIP) NA.8: 4 residues within 4Å: Chain A: N.405 Chain C: R.370, V.371, T.400 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.400, A:N.405 Water bridges: C:C.399 NA.14: 3 residues within 4Å: Chain B: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.482, B:Q.482 NA.15: 2 residues within 4Å: Chain B: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.9 No protein-ligand interaction detected (PLIP) NA.16: 4 residues within 4Å: Chain A: R.370, V.371, T.400 Chain B: N.405 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.371, B:N.405 Water bridges: A:C.399 NA.22: 3 residues within 4Å: Chain C: A.453, S.480, Q.482 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.482, C:Q.482 NA.23: 2 residues within 4Å: Chain C: G.99 Ligands: NDG-GLA-GLC-RAM-NAG.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.99 NA.24: 4 residues within 4Å: Chain B: R.370, V.371, T.400 Chain C: N.405 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.400, C:N.405 Water bridges: B:C.399

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

2016-03-09

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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