SMTL ID : 6e0w.2 (1 other biounit)

Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x BGC- FUC- FUC- GLA- BDP: beta-D-glucopyranuronic acid-(1-3)-alpha-D-galactopyranose-(1-3)-alpha-L-fucopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-beta-D-glucopyranose

BGC-FUC-FUC-GLA-BDP.1: 14 residues within 4Å: Chain A: Q.162, Y.182, L.185, Q.187, E.212, N.214, A.241, N.242, W.243, I.245, A.250, H.283, E.285 Ligands: HLA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.162, A:N.242, A:Q.187, A:Q.187 Water bridges: A:Y.135, A:K.137, A:K.137, A:K.137, A:Y.182, A:Y.182, A:N.214, A:N.214, A:E.285, A:T.156 BGC-FUC-FUC-GLA-BDP.13: 14 residues within 4Å: Chain B: Q.162, Y.182, L.185, Q.187, E.212, N.214, A.241, N.242, W.243, I.245, A.250, H.283, E.285 Ligands: HLA.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.162, B:N.242, B:Q.187, B:Q.187 Water bridges: B:Y.135, B:K.137, B:K.137, B:K.137, B:Y.182, B:Y.182, B:N.214, B:N.214, B:E.285, B:T.156 BGC-FUC-FUC-GLA-BDP.25: 14 residues within 4Å: Chain C: Q.162, Y.182, L.185, Q.187, E.212, N.214, A.241, N.242, W.243, I.245, A.250, H.283, E.285 Ligands: HLA.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.162, C:N.242, C:Q.187, C:Q.187 Water bridges: C:Y.135, C:K.137, C:K.137, C:K.137, C:Y.182, C:Y.182, C:N.214, C:N.214, C:E.285, C:T.156

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.279, S.304, T.305, G.306 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: R.279, L.309, T.310, T.311, R.340 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: N.242, Q.280, H.283, G.308, L.309, T.310, Y.317 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: N.114, G.115, G.116, T.117 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: R.130, N.152, Y.178 Ligands: PG4.23 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: R.88 Chain B: R.88 Chain C: R.88 Ligands: SO4.19, SO4.31 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.279, S.304, T.305, G.306 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: R.279, L.309, T.310, T.311, R.340 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain B: N.242, Q.280, H.283, G.308, L.309, T.310, Y.317 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: N.114, G.115, G.116, T.117 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: R.130, N.152, Y.178 Ligands: PG4.35 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain A: R.88 Chain B: R.88 Chain C: R.88 Ligands: SO4.7, SO4.31 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: R.279, S.304, T.305, G.306 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain C: R.279, L.309, T.310, T.311, R.340 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain C: N.242, Q.280, H.283, G.308, L.309, T.310, Y.317 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: N.114, G.115, G.116, T.117 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: R.130, N.152, Y.178 Ligands: PG4.11 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain A: R.88 Chain B: R.88 Chain C: R.88 Ligands: SO4.7, SO4.19 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.8: 1 residues within 4Å: Chain B: E.323 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain C: E.323 No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain A: E.323 No protein-ligand interaction detected (PLIP) MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.10: 2 residues within 4Å: Chain A: Y.276, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.300 Water bridges: A:N.277, A:N.277 EDO.22: 2 residues within 4Å: Chain B: Y.276, N.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.300 Water bridges: B:N.277, B:N.277 EDO.34: 2 residues within 4Å: Chain C: Y.276, N.300 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.300 Water bridges: C:N.277, C:N.277

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 7 residues within 4Å: Chain A: S.123, D.142, R.144 Chain C: R.130, E.176, Y.178 Ligands: SO4.30 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.130, C:R.130, C:Y.178, A:S.123 Water bridges: A:R.105, A:D.142 PG4.23: 7 residues within 4Å: Chain A: R.130, E.176, Y.178 Chain B: S.123, D.142, R.144 Ligands: SO4.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.123, A:R.130, A:R.130, A:Y.178 Water bridges: B:R.105, B:D.142 PG4.35: 7 residues within 4Å: Chain B: R.130, E.176, Y.178 Chain C: S.123, D.142, R.144 Ligands: SO4.18 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.130, B:R.130, B:Y.178, C:S.123 Water bridges: C:R.105, C:D.142

3 x HLA: 1,5-anhydro-4,6-O-[(1R)-1-carboxyethylidene]-D-galactitol(Non-covalent)

HLA.12: 4 residues within 4Å: Chain A: S.98, M.118, K.137 Ligands: BGC-FUC-FUC-GLA-BDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.98, A:K.137, A:K.137 Water bridges: A:M.118, A:Y.135 HLA.24: 4 residues within 4Å: Chain B: S.98, M.118, K.137 Ligands: BGC-FUC-FUC-GLA-BDP.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.98, B:K.137, B:K.137 Water bridges: B:M.118, B:Y.135 HLA.36: 4 residues within 4Å: Chain C: S.98, M.118, K.137 Ligands: BGC-FUC-FUC-GLA-BDP.25 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.98, C:K.137, C:K.137 Water bridges: C:M.118, C:Y.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Browning, C. et al., Crystal structure of the colanidase tailspike protein gp150 of Phage Phi92 complexed with one repeating unit of colanic acid. To Be Published

Release Date

2019-07-17

Peptides

Bacteriophage Phi92 gp150: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Bacteriophage Phi92 gp150

Related Entries With Identical Sequence