SMTL ID : 4ru4.1 (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

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

EDO.1: 7 residues within 4Å: Chain A: P.102, T.103, G.215, G.216, T.217, V.218, P.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.215, A:T.217, A:V.218 Water bridges: A:T.217 EDO.2: 6 residues within 4Å: Chain A: N.260, I.261, S.262, K.287, Y.289 Chain B: E.172 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.287, A:K.287, B:E.172 Water bridges: A:N.260, A:V.288 EDO.3: 9 residues within 4Å: Chain A: Y.45, P.46, H.47, A.48, W.57, A.58, Q.61, A.62, D.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.47, A:A.48, A:A.62 Water bridges: A:D.65 EDO.13: 7 residues within 4Å: Chain B: D.235, V.236, T.237, N.258, S.259, N.260 Chain C: R.232 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.260, C:R.232 Water bridges: B:D.235, B:D.235, B:D.235, B:D.235, B:D.235 EDO.14: 6 residues within 4Å: Chain B: N.260, I.261, S.262, K.287, Y.289 Chain C: E.172 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.172, B:N.260, B:K.287 Water bridges: C:S.230, C:S.230, B:V.288 EDO.15: 6 residues within 4Å: Chain B: R.162, Y.271, I.274, G.298, G.299, H.332 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.271, B:G.299 Water bridges: B:S.164, B:G.299 EDO.16: 8 residues within 4Å: Chain B: Y.45, P.46, H.47, W.57, A.58, Q.61, A.62, D.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.47, B:A.58 Water bridges: B:D.65 EDO.17: 3 residues within 4Å: Chain B: H.29, E.33, R.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.34 Water bridges: B:E.33 EDO.24: 7 residues within 4Å: Chain A: R.232 Chain C: D.235, V.236, T.237, N.258, S.259, N.260 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.260, A:R.232 Water bridges: C:D.235, C:D.235, C:T.237 EDO.25: 7 residues within 4Å: Chain A: E.172, R.184 Chain C: N.260, I.261, S.262, K.287, Y.289 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.260, C:K.287, A:E.172 Water bridges: C:V.288, A:S.230, A:S.230

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

NA.4: 3 residues within 4Å: Chain A: S.262 Chain B: G.145, R.184 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.184, B:R.184, A:S.262, A:S.262 NA.5: 2 residues within 4Å: Chain A: V.64, S.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88 Water bridges: A:D.65 NA.6: 2 residues within 4Å: Chain A: R.162, S.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.164, A:S.164 Water bridges: A:S.164 NA.7: 3 residues within 4Å: Chain A: G.145, R.184 Chain C: S.262 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.262, A:R.184, A:R.184 NA.8: 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.9: 1 residues within 4Å: Chain A: Q.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.42 NA.10: 3 residues within 4Å: Chain A: R.553, V.589, T.590 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.553, A:T.590, A:T.590 NA.18: 1 residues within 4Å: Chain B: A.375 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.409, B:A.410 NA.19: 4 residues within 4Å: Chain B: S.262, I.264 Chain C: G.145, R.184 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.144, C:R.184, C:R.184, B:S.262 NA.20: 3 residues within 4Å: Chain B: R.162, T.163, S.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.163, B:S.164 NA.21: 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.22: 3 residues within 4Å: Chain B: R.553, V.589, T.590 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.553, B:T.590 NA.26: 1 residues within 4Å: Chain C: Q.42 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.42 Water bridges: C:Q.42 NA.27: 3 residues within 4Å: Chain C: R.553, V.589, T.590 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.590, C:T.590

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

CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.12: 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.8, H2O.11, H2O.19, H2O.36 CA.23: 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.41, H2O.49, H2O.53, H2O.55 CA.28: 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.80, H2O.85, H2O.92, H2O.102

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
A

B
B

C
C

tail spike protein gp49

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