SMTL ID : 4ru4.2 (1 other biounit)

Crystal structure of the tailspike protein gp49 from Pseudomonas phage LKA1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Y.45, P.46, H.47, A.48, A.58, Q.61, A.62, D.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.45, A:H.47, A:A.58, A:A.62 EDO.2: 7 residues within 4Å: Chain A: D.235, V.236, T.237, N.258, S.259, N.260 Chain C: R.232 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.258, C:R.232 Water bridges: A:D.235, A:D.235 EDO.8: 7 residues within 4Å: Chain B: P.102, T.103, G.215, G.216, T.217, V.218, P.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.217, B:V.218 Water bridges: B:T.217, B:T.217 EDO.9: 4 residues within 4Å: Chain A: N.566 Chain B: R.553, S.554, Y.555 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.553, B:S.554, B:Y.555, A:N.566 Water bridges: B:D.552, B:S.554, B:Y.555, A:N.566 EDO.10: 9 residues within 4Å: Chain B: Y.45, P.46, H.47, A.48, W.57, A.58, Q.61, A.62, D.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.47, B:H.47, B:A.48, B:A.62 Water bridges: B:D.65 EDO.16: 6 residues within 4Å: Chain B: E.172 Chain C: N.260, I.261, S.262, K.287, Y.289 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.260, C:K.287, C:K.287, B:E.172 Water bridges: C:V.288 EDO.17: 7 residues within 4Å: Chain B: R.232 Chain C: D.235, V.236, T.237, N.258, S.259, N.260 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.260, B:R.232 Water bridges: C:D.235 EDO.18: 8 residues within 4Å: Chain C: Y.45, P.46, H.47, W.57, A.58, Q.61, A.62, D.65 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.47, C:A.48, C:A.58, C:A.62 Water bridges: C:H.47, C:D.65

7 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: G.145, R.184 Chain B: S.262 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.262, B:S.262, A:R.184, A:R.184 NA.4: 3 residues within 4Å: Chain A: S.262 Chain C: G.145, R.184 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.262, C:A.144, C:R.184, C:R.184 NA.5: 2 residues within 4Å: Chain A: A.50, L.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.51 Water bridges: A:S.52 NA.11: 3 residues within 4Å: Chain B: R.162, T.163, S.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.163, B:S.164, B:S.164 Water bridges: B:S.164 NA.12: 4 residues within 4Å: Chain B: A.144, G.145, R.184 Chain C: S.262 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.262, B:A.144, B:R.184, B:R.184 NA.13: 2 residues within 4Å: Chain B: A.50, L.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.51 Water bridges: B:S.52 NA.14: 3 residues within 4Å: Chain B: S.85, T.86, S.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.85, B:S.88, B:S.88 Water bridges: B:T.86

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

CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: G.368, D.394 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.368, A:D.394, H2O.4, H2O.9, H2O.16, H2O.21 CA.15: 2 residues within 4Å: Chain B: G.368, D.394 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.368, B:D.394, H2O.44, H2O.46, H2O.58, H2O.68 CA.19: 2 residues within 4Å: Chain C: G.368, D.394 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:G.368, C:D.394, H2O.76, H2O.81, H2O.86, H2O.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olszak, T. et al., The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence. Sci Rep (2017)

Release Date

2015-11-18

Peptides

tail spike protein gp49: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

tail spike protein gp49

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