SMTL ID : 2vbe.1

Tailspike protein of bacteriophage Sf6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-trimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.27, H.45 Chain C: K.33 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.27, A:H.45, H2O.24, H2O.24, H2O.24, H2O.24 MN.12: 3 residues within 4Å: Chain A: K.33 Chain B: D.27, H.45 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.27, B:H.45, H2O.48, H2O.48, H2O.48, H2O.48 MN.23: 3 residues within 4Å: Chain B: K.33 Chain C: D.27, H.45 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.27, C:H.45, H2O.72, H2O.72, H2O.72, H2O.72

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.13, CA.24 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.286, C:E.286, B:E.286, H2O.15, H2O.39, H2O.63 CA.3: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.14, CA.25 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:E.286, C:E.286, H2O.15, H2O.39, H2O.64 CA.13: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.2, CA.24 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.286, C:E.286, B:E.286, H2O.15, H2O.39, H2O.63 CA.14: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.3, CA.25 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.15, H2O.39, H2O.64 CA.24: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.2, CA.13 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.286, C:E.286, B:E.286, H2O.15, H2O.39, H2O.63 CA.25: 5 residues within 4Å: Chain A: E.286 Chain B: E.286 Chain C: E.286 Ligands: CA.3, CA.14 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:E.286, C:E.286, H2O.15, H2O.39, H2O.64

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: I.52, L.81, G.85, E.86 Chain B: A.91, V.115 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: N.154, T.155, E.187, Y.233 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: V.219, E.258, A.259, L.281, D.282 Chain B: D.289, D.291, W.313 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: A.79, P.107 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: S.474, F.476, D.484, K.485, V.486 Chain B: F.476 Ligands: EDO.19, EDO.30 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: G.101, S.102, L.127, T.128 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: I.52, L.81, G.85, E.86 Chain C: A.91, V.115 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: N.154, T.155, E.187, Y.233 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: V.219, E.258, A.259, L.281, D.282 Chain C: D.289, D.291, W.313 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: A.79, P.107 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: S.474, F.476, D.484, K.485, V.486 Chain C: F.476 Ligands: EDO.8, EDO.30 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: G.101, S.102, L.127, T.128 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: A.91, V.115 Chain C: I.52, L.81, G.85, E.86 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: N.154, T.155, E.187, Y.233 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: D.289, D.291, W.313 Chain C: V.219, E.258, A.259, L.281, D.282 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain C: A.79, P.107 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain A: F.476 Chain C: S.474, F.476, D.484, K.485, V.486 Ligands: EDO.8, EDO.19 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: G.101, S.102, L.127, T.128 Ligand excluded by PLIP

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

PO4.10: 4 residues within 4Å: Chain A: D.167, S.168, V.169, R.171 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.166, A:S.168, A:V.169 Water bridges: A:Y.136, A:D.167, A:D.167 Salt bridges: A:R.171 PO4.11: 5 residues within 4Å: Chain A: R.42, D.46, K.49 Chain B: L.55, V.59 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.46, A:D.46 Water bridges: A:R.42, B:V.59 Salt bridges: A:R.42, A:K.49 PO4.21: 4 residues within 4Å: Chain B: D.167, S.168, V.169, R.171 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.166, B:S.168, B:V.169 Water bridges: B:Y.136, B:D.167, B:D.167 Salt bridges: B:R.171 PO4.22: 5 residues within 4Å: Chain B: R.42, D.46, K.49 Chain C: L.55, V.59 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Water bridges: C:V.59, B:R.42 Hydrogen bonds: B:D.46, B:D.46 Salt bridges: B:R.42, B:K.49 PO4.32: 4 residues within 4Å: Chain C: D.167, S.168, V.169, R.171 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.166, C:S.168, C:V.169 Water bridges: C:Y.136, C:D.167, C:D.167 Salt bridges: C:R.171 PO4.33: 5 residues within 4Å: Chain A: L.55, V.59 Chain C: R.42, D.46, K.49 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.46, C:D.46 Water bridges: C:R.42, A:V.59 Salt bridges: C:R.42, C:K.49

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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