SMTL ID : 4y9v.1

Gp54 tailspike of Acinetobacter baumannii bacteriophage AP22 in complex with A. baumannii capsular saccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.90 Å

Oligo State

homo-trimer

Ligands

3 x 49S- 49T- 49V: 2-acetamido-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-alpha-D-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-mannopyranuronic acid

49S-49T-49V.1: 14 residues within 4Å: Chain A: R.166, Y.168, Y.169, F.249, T.275, L.276, Y.278, Q.281, G.305, G.306, D.307, G.308, H.337 Ligands: SO4.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.168, A:Y.169, A:Y.168, A:F.249, A:L.276 Hydrogen bonds: A:R.166, A:Y.168, A:Y.168, A:Y.278, A:Q.281, A:G.306 Water bridges: A:T.275, A:T.275, A:R.253, A:R.253, A:R.253, A:R.253, A:D.307 Salt bridges: A:R.166, A:H.337 49S-49T-49V.15: 14 residues within 4Å: Chain B: R.166, Y.168, Y.169, F.249, T.275, L.276, Y.278, Q.281, G.305, G.306, D.307, G.308, H.337 Ligands: SO4.24 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.168, B:Y.169, B:Y.168, B:F.249, B:L.276 Hydrogen bonds: B:R.166, B:Y.168, B:Y.168, B:Y.278, B:Q.281, B:G.306 Water bridges: B:T.275, B:T.275, B:R.253, B:R.253, B:R.253, B:R.253, B:D.307 Salt bridges: B:R.166, B:H.337 49S-49T-49V.29: 14 residues within 4Å: Chain C: R.166, Y.168, Y.169, F.249, T.275, L.276, Y.278, Q.281, G.305, G.306, D.307, G.308, H.337 Ligands: SO4.38 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.168, C:Y.169, C:Y.168, C:F.249, C:L.276 Hydrogen bonds: C:R.166, C:Y.168, C:Y.168, C:Y.278, C:Q.281, C:G.306 Water bridges: C:T.275, C:T.275, C:R.253, C:R.253, C:R.253, C:R.253, C:D.307 Salt bridges: C:R.166, C:H.337

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

EDO.2: 5 residues within 4Å: Chain A: D.48, L.51, K.52, P.58 Ligands: EDO.8 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: K.132, Y.162, E.341, A.357, G.358, D.359, R.382, G.383 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: I.209, N.210, F.211, I.231, A.234, F.237 Ligands: EDO.7 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.50, K.53, Q.68, D.72 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: H.46, H.78, V.79, K.80, E.101 Chain B: L.43 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.210, R.235, N.236, F.237 Chain C: Y.241 Ligands: EDO.4 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: D.48 Chain B: I.35, E.39, L.43 Ligands: EDO.2 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: D.42, A.45, V.74, K.75, K.76 Chain C: E.101 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: D.48, L.51, K.52, P.58 Ligands: EDO.22 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: K.132, Y.162, E.341, A.357, G.358, D.359, R.382, G.383 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: I.209, N.210, F.211, I.231, A.234, F.237 Ligands: EDO.21 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: Y.50, K.53, Q.68, D.72 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: H.46, H.78, V.79, K.80, E.101 Chain C: L.43 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: Y.241 Chain B: N.210, R.235, N.236, F.237 Ligands: EDO.18 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: D.48 Chain C: I.35, E.39, L.43 Ligands: EDO.16 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: E.101 Chain B: D.42, A.45, V.74, K.75, K.76 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: D.48, L.51, K.52, P.58 Ligands: EDO.36 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: K.132, Y.162, E.341, A.357, G.358, D.359, R.382, G.383 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: I.209, N.210, F.211, I.231, A.234, F.237 Ligands: EDO.35 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: Y.50, K.53, Q.68, D.72 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: L.43 Chain C: H.46, H.78, V.79, K.80, E.101 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: Y.241 Chain C: N.210, R.235, N.236, F.237 Ligands: EDO.32 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: I.35, E.39, L.43 Chain C: D.48 Ligands: EDO.30 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain B: E.101 Chain C: D.42, A.45, V.74, K.75, K.76 Ligand excluded by PLIP

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

SO4.10: 6 residues within 4Å: Chain A: R.166, Y.278, R.299, H.300, H.337 Ligands: 49S-49T-49V.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.278 Water bridges: A:R.166, A:R.166 Salt bridges: A:R.166, A:R.299, A:H.300, A:H.337 SO4.11: 2 residues within 4Å: Chain A: R.540, R.599 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.540, A:R.540, A:R.540, A:R.599, A:R.599, A:R.599 Salt bridges: A:R.540, A:R.599 SO4.24: 6 residues within 4Å: Chain B: R.166, Y.278, R.299, H.300, H.337 Ligands: 49S-49T-49V.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.278 Water bridges: B:R.166, B:R.166 Salt bridges: B:R.166, B:R.299, B:H.300, B:H.337 SO4.25: 2 residues within 4Å: Chain B: R.540, R.599 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.540, B:R.540, B:R.540, B:R.599, B:R.599, B:R.599 Salt bridges: B:R.540, B:R.599 SO4.38: 6 residues within 4Å: Chain C: R.166, Y.278, R.299, H.300, H.337 Ligands: 49S-49T-49V.29 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.278 Water bridges: C:R.166, C:R.166 Salt bridges: C:R.166, C:R.299, C:H.300, C:H.337 SO4.39: 2 residues within 4Å: Chain C: R.540, R.599 8 PLIP interactions: 8 interactions with chain C Water bridges: C:R.540, C:R.540, C:R.540, C:R.599, C:R.599, C:R.599 Salt bridges: C:R.540, C:R.599

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 8 residues within 4Å: Chain A: P.582, N.605 Chain B: P.582, N.605 Chain C: P.582, N.605 Ligands: CL.26, CL.40 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: S.568 Chain B: L.592 Ligand excluded by PLIP CL.26: 8 residues within 4Å: Chain A: P.582, N.605 Chain B: P.582, N.605 Chain C: P.582, N.605 Ligands: CL.12, CL.40 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: S.568 Chain C: L.592 Ligand excluded by PLIP CL.40: 8 residues within 4Å: Chain A: P.582, N.605 Chain B: P.582, N.605 Chain C: P.582, N.605 Ligands: CL.12, CL.26 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain A: L.592 Chain C: S.568 Ligand excluded by PLIP

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

NA.13: 2 residues within 4Å: Ligands: NA.27, NA.41 10 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 4 interactions with chain B Water bridges: C:D.422, C:D.422, C:D.422, A:D.422, A:D.422, A:G.459, B:D.422, B:D.422, B:D.422, B:G.459 NA.27: 2 residues within 4Å: Ligands: NA.13, NA.41 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Water bridges: A:D.422, A:G.459, B:D.422, B:D.422, B:D.422, B:D.422, B:D.422 NA.41: 2 residues within 4Å: Ligands: NA.13, NA.27 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Water bridges: C:D.422, A:D.422, B:D.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buth, S.A. et al., Structure of Acinetobacter baumannii bacteriophage AP22 polysaccharide degrading lyase in complex with A. baumannii capsular saccharide at 0.9 A resolution. TO BE PUBLISHED

Release Date

2017-02-01

Peptides

Particle-associated lyase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Particle-associated lyase