SMTL ID : 4ru5.1

Crystal Structure of the Pseudomonas phage phi297 tailspike gp61

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-trimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: R.242, N.269, D.270, E.271 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.242, A:D.270, A:E.271, H2O.4, H2O.5 CA.2: 4 residues within 4Å: Chain A: D.323, I.324, D.327, S.369 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.323, A:I.324, A:D.327, H2O.6, H2O.7 CA.14: 4 residues within 4Å: Chain B: R.242, N.269, D.270, E.271 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.242, B:D.270, B:E.271, H2O.41, H2O.44 CA.15: 4 residues within 4Å: Chain B: D.323, I.324, D.327, S.369 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.323, B:I.324, B:D.327, H2O.45, H2O.48 CA.24: 4 residues within 4Å: Chain C: R.242, N.269, D.270, E.271 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:R.242, C:D.270, C:E.271, H2O.87, H2O.89 CA.25: 4 residues within 4Å: Chain C: D.323, I.324, D.327, S.369 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.323, C:I.324, C:D.327, H2O.86, H2O.93

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

NA.3: 1 residues within 4Å: Chain B: A.567 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:A.567, B:A.567 Water bridges: A:A.567, C:A.567 NA.4: 2 residues within 4Å: Chain A: E.193, D.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.195 Water bridges: A:D.195 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain A: R.160, D.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.161, A:D.161 NA.7: 3 residues within 4Å: Chain A: D.139, R.200 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.139, A:R.200 NA.8: 4 residues within 4Å: Chain A: D.139, R.198, R.200 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.139, A:R.198, A:R.200, A:R.200 Water bridges: A:R.198 NA.16: 2 residues within 4Å: Chain A: S.558 Chain B: Y.570 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.570, A:S.558 NA.17: 1 residues within 4Å: Chain B: Y.243 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.218, B:N.269, B:D.270 NA.26: 1 residues within 4Å: Chain C: M.460 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Water bridges: A:N.482, C:V.458, C:H.459, C:A.461, C:Y.490 Hydrogen bonds: C:M.460 NA.27: 3 residues within 4Å: Chain C: T.33, L.34, A.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.34, C:A.35

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

EDO.9: 8 residues within 4Å: Chain A: D.91, G.92, Y.93, A.94 Chain B: D.85, I.86, R.87, R.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.93, A:A.94, A:Y.236 EDO.10: 5 residues within 4Å: Chain A: T.523, S.525, T.527, V.528, A.529 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.523, A:S.525, A:A.529 EDO.11: 3 residues within 4Å: Chain A: H.43, T.45, R.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.45, A:T.45, A:R.78, A:R.78 Water bridges: A:P.42 EDO.12: 2 residues within 4Å: Chain A: K.14, D.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.14 Water bridges: A:D.15 EDO.18: 8 residues within 4Å: Chain B: D.91, G.92, Y.93, A.94 Chain C: D.85, I.86, R.87, R.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.93, B:A.94 Water bridges: B:Y.236 EDO.19: 5 residues within 4Å: Chain B: D.159, G.410, T.411, S.412, R.443 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.412, B:S.412, B:R.443, B:R.443 Water bridges: B:G.410, B:G.410 EDO.20: 5 residues within 4Å: Chain B: A.267, V.268, R.293, I.324, S.326 4 PLIP interactions: 4 interactions with chain B Water bridges: B:V.268, B:R.293, B:R.293, B:R.293 EDO.28: 2 residues within 4Å: Chain C: Q.117, D.195 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.117, C:D.195 EDO.29: 8 residues within 4Å: Chain A: D.85, I.86, R.87, R.203 Chain C: D.91, G.92, Y.93, A.94 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.93, C:A.94 Water bridges: C:Y.236, C:Y.236 EDO.30: 4 residues within 4Å: Chain C: T.527, A.529, Y.570, R.578 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.578 Water bridges: C:T.527, C:T.527, C:R.578 EDO.31: 2 residues within 4Å: Chain C: D.15, Y.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.15 EDO.32: 5 residues within 4Å: Chain C: D.159, G.410, T.411, S.412, R.443 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.411, C:S.412, C:S.412, C:R.443, C:R.443 Water bridges: C:D.159, C:D.159, C:G.410, C:G.410 EDO.33: 4 residues within 4Å: Chain C: A.267, V.268, R.293, I.324 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.293

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 3 residues within 4Å: Chain A: A.218, R.242, N.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.269 Salt bridges: A:R.242 ACT.21: 3 residues within 4Å: Chain B: A.218, R.242, N.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.269 Salt bridges: B:R.242 ACT.22: 4 residues within 4Å: Chain B: S.192, E.193, V.194, D.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.192 Water bridges: B:D.195, B:D.195, B:D.195 ACT.23: 3 residues within 4Å: Chain B: A.532, Q.533, T.534 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.533, B:T.534 Water bridges: B:Q.533, B:Q.533 ACT.34: 3 residues within 4Å: Chain C: A.218, R.242, N.269 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.218 Hydrogen bonds: C:N.269 Salt bridges: C:R.242 ACT.35: 3 residues within 4Å: Chain C: D.302, A.303, V.304 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.303 Hydrogen bonds: C:V.304 Water bridges: C:R.250 ACT.36: 3 residues within 4Å: Chain C: A.532, Q.533, T.534 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.533, C:T.534, C:T.534, C:T.534

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

tailspike gp27: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

tailspike gp27