SMTL ID : 2vbm.1

Tailspike protein of bacteriophage Sf6 complexed with tetrasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x RAM- RAM- NAG- RAM: alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose

RAM-RAM-NAG-RAM.1: 10 residues within 4Å: Chain A: A.95, R.122, R.149, E.185, T.207 Chain C: S.138, D.139, T.140, Q.172, Y.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.95 Hydrogen bonds: A:R.122, A:R.122, A:R.149, A:E.185 Water bridges: A:R.149 RAM-RAM-NAG-RAM.7: 10 residues within 4Å: Chain A: S.138, D.139, T.140, Q.172, Y.174 Chain B: A.95, R.122, R.149, E.185, T.207 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.95 Hydrogen bonds: B:R.122, B:R.122, B:R.149, B:E.185 Water bridges: B:R.149 RAM-RAM-NAG-RAM.13: 10 residues within 4Å: Chain B: S.138, D.139, T.140, Q.172, Y.174 Chain C: A.95, R.122, R.149, E.185, T.207 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.95 Hydrogen bonds: C:R.122, C:R.122, C:R.149, C:E.185 Water bridges: C:R.149

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: D.167, S.168, V.169, R.171 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.167, A:D.167, A:S.168, A:V.169 Water bridges: A:T.164 Salt bridges: A:R.171 PO4.3: 5 residues within 4Å: Chain A: R.42, D.46, K.49 Chain B: L.55, V.59 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.42, A:K.49 Hydrogen bonds: B:L.55 PO4.8: 4 residues within 4Å: Chain B: D.167, S.168, V.169, R.171 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.167, B:D.167, B:S.168, B:V.169 Water bridges: B:T.164 Salt bridges: B:R.171 PO4.9: 5 residues within 4Å: Chain B: R.42, D.46, K.49 Chain C: L.55, V.59 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.42, B:K.49 Hydrogen bonds: C:L.55 PO4.14: 4 residues within 4Å: Chain C: D.167, S.168, V.169, R.171 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.167, C:D.167, C:S.168, C:V.169 Water bridges: C:T.164 Salt bridges: C:R.171 PO4.15: 5 residues within 4Å: Chain A: L.55, V.59 Chain C: R.42, D.46, K.49 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.42, C:K.49 Hydrogen bonds: A:L.55

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MG.10, MG.16 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.286, A:E.286, B:E.286, H2O.5, H2O.15, H2O.24 MG.10: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MG.4, MG.16 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.286, A:E.286, B:E.286, H2O.5, H2O.15, H2O.24 MG.16: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MG.4, MG.10 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.286, A:E.286, B:E.286, H2O.5, H2O.15, H2O.24

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MN.11, MN.17 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.286, B:E.286, H2O.10, H2O.19, H2O.29 MN.6: 4 residues within 4Å: Chain A: Q.15, D.27, H.45 Chain C: K.33 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.27, A:H.45, H2O.10 MN.11: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MN.5, MN.17 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:E.286, A:E.286, H2O.10, H2O.19, H2O.29 MN.12: 4 residues within 4Å: Chain A: K.33 Chain B: Q.15, D.27, H.45 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.27, B:H.45, H2O.19 MN.17: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: MN.5, MN.11 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.286, B:E.286, H2O.10, H2O.19, H2O.29 MN.18: 4 residues within 4Å: Chain B: K.33 Chain C: Q.15, D.27, H.45 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.27, C:H.45, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, J.J. et al., An Intersubunit Active Site between Supercoiled Parallel Beta Helices in the Trimeric Tailspike Endorhamnosidase of Shigella Flexneri Phage Sf6. Structure (2008)

Release Date

2008-04-22

Peptides

TAILSPIKE-PROTEIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

TAILSPIKE-PROTEIN

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