SMTL ID : 2vjj.1

TAILSPIKE PROTEIN OF E.COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-trimer

Ligands

3 x NAG- GAL- GLC- RAM- NAG- GLC: alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]beta-D-galactopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-GAL-GLC-RAM-NAG-GLC.1: 31 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, D.230, H.231, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: CA.2, K.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.288, A:S.320, A:D.321, A:G.359, A:N.362, A:N.206, A:N.206, A:N.237, A:E.291, A:H.103, A:Q.133 Water bridges: A:D.230, A:S.320, A:S.320, A:P.360, A:N.362, A:R.396, A:G.102 Hydrophobic interactions: A:F.138 NAG-GAL-GLC-RAM-NAG-GLC.12: 31 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, D.230, H.231, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: CA.13, K.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.288, B:S.320, B:D.321, B:G.359, B:N.362, B:N.206, B:N.206, B:N.237, B:E.291, B:H.103, B:Q.133 Water bridges: B:D.230, B:S.320, B:S.320, B:P.360, B:N.362, B:R.396, B:G.102 Hydrophobic interactions: B:F.138 NAG-GAL-GLC-RAM-NAG-GLC.23: 31 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, D.230, H.231, S.232, Y.235, N.237, E.263, Y.284, V.286, H.288, E.291, L.318, G.319, S.320, D.321, G.359, P.360, D.361, N.362 Ligands: CA.24, K.26 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.288, C:S.320, C:D.321, C:G.359, C:N.362, C:N.206, C:N.206, C:N.237, C:E.291, C:H.103, C:Q.133 Water bridges: C:D.230, C:S.320, C:S.320, C:P.360, C:N.362, C:R.396, C:G.102 Hydrophobic interactions: C:F.138

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: G.102 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.102, H2O.6, H2O.6, H2O.8, H2O.28 CA.13: 2 residues within 4Å: Chain B: G.102 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.102, H2O.34, H2O.34, H2O.36, H2O.56 CA.24: 2 residues within 4Å: Chain C: G.102 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.23 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:G.102, H2O.62, H2O.62, H2O.65, H2O.84

3 x CL: CHLORIDE ION(Non-covalent)(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: S.487, Y.488, G.514, A.515, N.516, V.517 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: S.487, Y.488, G.514, A.515, N.516, V.517 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain C: S.487, Y.488, G.514, A.515, N.516, V.517 Ligand excluded by PLIP

3 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.4: 4 residues within 4Å: Chain A: H.103, S.104, Q.133 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.1 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain B: H.103, S.104, Q.133 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.12 No protein-ligand interaction detected (PLIP) K.26: 4 residues within 4Å: Chain C: H.103, S.104, Q.133 Ligands: NAG-GAL-GLC-RAM-NAG-GLC.23 No protein-ligand interaction detected (PLIP)

21 x GOL: GLYCEROL(Non-functional Binders)(Non-covalent)

GOL.5: 4 residues within 4Å: Chain A: R.31, D.35 Chain B: W.44, V.54 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: Y.300, N.331, D.332 Chain B: V.310, S.341, E.344 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: N.460, Y.488 Chain B: E.470 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: D.38, E.39, R.40, V.41, G.79, G.80, T.81 Chain C: Y.22 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.598, Q.599 Chain B: K.499, S.555, I.556 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: T.524, S.591, V.592, R.593 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: D.432, E.464 Chain B: K.433, S.434, N.435, V.436, Q.466 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: R.31, D.35 Chain C: W.44, V.54 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: Y.300, N.331, D.332 Chain C: V.310, S.341, E.344 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: N.460, Y.488 Chain C: E.470 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: Y.22 Chain B: D.38, E.39, R.40, V.41, G.79, G.80, T.81 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: R.598, Q.599 Chain C: K.499, S.555, I.556 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: T.524, S.591, V.592, R.593 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: D.432, E.464 Chain C: K.433, S.434, N.435, V.436, Q.466 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: W.44, V.54 Chain C: R.31, D.35 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain A: V.310, S.341, E.344 Chain C: Y.300, N.331, D.332 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain A: E.470 Chain C: N.460, Y.488 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain B: Y.22 Chain C: D.38, E.39, R.40, V.41, G.79, G.80, T.81 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain A: K.499, S.555, I.556 Chain C: R.598, Q.599 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: T.524, S.591, V.592, R.593 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain A: K.433, S.434, N.435, V.436, Q.466 Chain C: D.432, E.464 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Barbirz, S. et al., Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related. Mol.Microbiol. (2008)

Release Date

2008-07-01

Peptides

TAILSPIKE PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

TAILSPIKE PROTEIN

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