SMTL ID : 4xla.1

Tailspike protein mutant D339A of E. coli bacteriophage HK620 IN COMPLEX WITH PENTASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 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: 24 residues within 4Å: Chain A: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, A.230, S.232, Y.235, N.237, E.263, H.265, Y.284, V.286, H.288, A.290, E.291, N.362 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.288, A:G.102, A:H.103 Hydrophobic interactions: A:A.290, A:E.291, A:F.138 Hydrogen bonds: A:G.204, A:N.206, A:N.206, A:N.237, A:E.291, A:H.103, A:Q.133 NAG-GLA-GLC-RAM-NAG.9: 24 residues within 4Å: Chain B: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, A.230, S.232, Y.235, N.237, E.263, H.265, Y.284, V.286, H.288, A.290, E.291, N.362 Ligands: NA.15 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.288, B:G.102, B:H.103 Hydrophobic interactions: B:A.290, B:E.291, B:F.138 Hydrogen bonds: B:G.204, B:N.206, B:N.206, B:N.237, B:E.291, B:H.103, B:Q.133 NAG-GLA-GLC-RAM-NAG.17: 24 residues within 4Å: Chain C: G.102, H.103, Q.133, F.138, L.173, T.198, W.199, T.202, G.204, W.205, N.206, A.230, S.232, Y.235, N.237, E.263, H.265, Y.284, V.286, H.288, A.290, E.291, N.362 Ligands: NA.23 5 PLIP interactions: 5 interactions with chain C Water bridges: C:H.288, C:G.102, C:H.103 Hydrophobic interactions: C:A.290, C:E.291, C:F.138 Hydrogen bonds: C:G.204, C:N.206, C:N.206, C:N.237, C:E.291, C:H.103, C:Q.133

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.459, N.460, Y.488 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.460 Water bridges: A:Q.427, B:E.470, B:E.470 TRS.10: 3 residues within 4Å: Chain B: V.459, N.460, Y.488 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.460 Water bridges: B:Q.427, C:E.470, C:E.470 TRS.18: 3 residues within 4Å: Chain C: V.459, N.460, Y.488 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:E.470, A:E.470, C:Q.427 Hydrogen bonds: C:N.460

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

FMT.3: 3 residues within 4Å: Chain A: N.559, L.560, D.561 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.560, A:D.561, A:D.561 FMT.4: 4 residues within 4Å: Chain A: L.560, E.583 Chain C: K.571, N.573 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.571, C:N.573 Water bridges: C:Q.575 FMT.5: 4 residues within 4Å: Chain A: R.31, D.35 Chain B: W.44, V.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.31 Water bridges: A:D.35, A:D.35 FMT.6: 3 residues within 4Å: Chain A: N.194, I.220, N.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.194, A:N.221 Water bridges: A:S.251 FMT.11: 3 residues within 4Å: Chain B: N.559, L.560, D.561 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.560, B:D.561, B:D.561 FMT.12: 4 residues within 4Å: Chain A: K.571, N.573 Chain B: L.560, E.583 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.571, A:N.573 Water bridges: A:Q.575 FMT.13: 4 residues within 4Å: Chain B: R.31, D.35 Chain C: W.44, V.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.31 Water bridges: B:D.35, B:D.35 FMT.14: 3 residues within 4Å: Chain B: N.194, I.220, N.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.194, B:N.221 Water bridges: B:S.251 FMT.19: 3 residues within 4Å: Chain C: N.559, L.560, D.561 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.560, C:D.561, C:D.561 FMT.20: 4 residues within 4Å: Chain B: K.571, N.573 Chain C: L.560, E.583 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.571, B:N.573 Water bridges: B:Q.575 FMT.21: 4 residues within 4Å: Chain A: W.44, V.54 Chain C: R.31, D.35 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.31 Water bridges: C:D.35, C:D.35 FMT.22: 3 residues within 4Å: Chain C: N.194, I.220, N.221 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.194, C:N.221 Water bridges: C:S.251

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

NA.7: 2 residues within 4Å: Chain A: G.102 Ligands: NAG-GLA-GLC-RAM-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.102 NA.8: 3 residues within 4Å: Chain A: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.483, A:Q.485 NA.15: 2 residues within 4Å: Chain B: G.102 Ligands: NAG-GLA-GLC-RAM-NAG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.102 NA.16: 3 residues within 4Å: Chain B: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.485, B:Q.485 NA.23: 2 residues within 4Å: Chain C: G.102 Ligands: NAG-GLA-GLC-RAM-NAG.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.102 NA.24: 3 residues within 4Å: Chain C: A.456, S.483, Q.485 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.485, C:Q.485

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

2016-01-20

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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