SMTL ID : 4mtm.1

Crystal structure of the tail fiber gp53 from Acinetobacter baumannii bacteriophage AP22

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-trimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: S.75, G.90, V.91, F.92, T.93, N.100, L.101, I.102, P.104, W.159 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.75, A:V.91, A:I.102, A:W.159 Water bridges: A:V.91, A:T.93 GOL.28: 10 residues within 4Å: Chain B: S.75, G.90, V.91, F.92, T.93, N.100, L.101, I.102, P.104, W.159 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.75, B:V.91, B:I.102, B:W.159 Water bridges: B:V.91, B:T.93 GOL.55: 10 residues within 4Å: Chain C: S.75, G.90, V.91, F.92, T.93, N.100, L.101, I.102, P.104, W.159 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.75, C:V.91, C:I.102, C:W.159 Water bridges: C:V.91, C:T.93

60 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.2: 3 residues within 4Å: Chain A: V.44, L.45, N.46 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: N.43, V.44 Chain C: S.33 Ligand excluded by PLIP BR.4: 3 residues within 4Å: Chain A: N.46 Chain B: K.60 Ligands: BR.5 Ligand excluded by PLIP BR.5: 4 residues within 4Å: Chain A: N.48 Chain B: K.60 Ligands: BR.4, BR.18 Ligand excluded by PLIP BR.6: 4 residues within 4Å: Chain A: F.68, Q.69, R.79, G.81 Ligand excluded by PLIP BR.7: 3 residues within 4Å: Chain A: N.73, Q.74, S.75 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: T.95, K.96, S.153 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain A: S.99, N.100, K.141 Ligand excluded by PLIP BR.10: 2 residues within 4Å: Chain A: N.100, I.102 Ligand excluded by PLIP BR.11: 7 residues within 4Å: Chain A: P.123, D.124, V.125 Chain C: Q.146, V.147, G.148 Ligands: EDO.79 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: Q.74, V.91, K.156 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Chain A: K.40 Chain C: A.36 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain A: D.131, L.132, S.133 Chain B: N.119 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain A: N.48 Chain B: K.60 Ligands: BR.18 Ligand excluded by PLIP BR.16: 2 residues within 4Å: Chain A: L.105, A.106 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain A: K.96, L.152, S.153 Ligand excluded by PLIP BR.18: 4 residues within 4Å: Chain A: N.48 Chain B: K.60 Ligands: BR.5, BR.15 Ligand excluded by PLIP BR.19: 3 residues within 4Å: Chain A: T.136, K.137 Ligands: BR.20 Ligand excluded by PLIP BR.20: 3 residues within 4Å: Chain A: K.137 Ligands: BR.19, BR.21 Ligand excluded by PLIP BR.21: 2 residues within 4Å: Chain A: K.137 Ligands: BR.20 Ligand excluded by PLIP BR.29: 3 residues within 4Å: Chain B: V.44, L.45, N.46 Ligand excluded by PLIP BR.30: 3 residues within 4Å: Chain A: S.33 Chain B: N.43, V.44 Ligand excluded by PLIP BR.31: 3 residues within 4Å: Chain B: N.46 Chain C: K.60 Ligands: BR.32 Ligand excluded by PLIP BR.32: 4 residues within 4Å: Chain B: N.48 Chain C: K.60 Ligands: BR.31, BR.45 Ligand excluded by PLIP BR.33: 4 residues within 4Å: Chain B: F.68, Q.69, R.79, G.81 Ligand excluded by PLIP BR.34: 3 residues within 4Å: Chain B: N.73, Q.74, S.75 Ligand excluded by PLIP BR.35: 3 residues within 4Å: Chain B: T.95, K.96, S.153 Ligand excluded by PLIP BR.36: 3 residues within 4Å: Chain B: S.99, N.100, K.141 Ligand excluded by PLIP BR.37: 2 residues within 4Å: Chain B: N.100, I.102 Ligand excluded by PLIP BR.38: 7 residues within 4Å: Chain A: Q.146, V.147, G.148 Chain B: P.123, D.124, V.125 Ligands: EDO.25 Ligand excluded by PLIP BR.39: 3 residues within 4Å: Chain B: Q.74, V.91, K.156 Ligand excluded by PLIP BR.40: 2 residues within 4Å: Chain A: A.36 Chain B: K.40 Ligand excluded by PLIP BR.41: 4 residues within 4Å: Chain B: D.131, L.132, S.133 Chain C: N.119 Ligand excluded by PLIP BR.42: 3 residues within 4Å: Chain B: N.48 Chain C: K.60 Ligands: BR.45 Ligand excluded by PLIP BR.43: 2 residues within 4Å: Chain B: L.105, A.106 Ligand excluded by PLIP BR.44: 3 residues within 4Å: Chain B: K.96, L.152, S.153 Ligand excluded by PLIP BR.45: 4 residues within 4Å: Chain B: N.48 Chain C: K.60 Ligands: BR.32, BR.42 Ligand excluded by PLIP BR.46: 3 residues within 4Å: Chain B: T.136, K.137 Ligands: BR.47 Ligand excluded by PLIP BR.47: 3 residues within 4Å: Chain B: K.137 Ligands: BR.46, BR.48 Ligand excluded by PLIP BR.48: 2 residues within 4Å: Chain B: K.137 Ligands: BR.47 Ligand excluded by PLIP BR.56: 3 residues within 4Å: Chain C: V.44, L.45, N.46 Ligand excluded by PLIP BR.57: 3 residues within 4Å: Chain B: S.33 Chain C: N.43, V.44 Ligand excluded by PLIP BR.58: 3 residues within 4Å: Chain A: K.60 Chain C: N.46 Ligands: BR.59 Ligand excluded by PLIP BR.59: 4 residues within 4Å: Chain A: K.60 Chain C: N.48 Ligands: BR.58, BR.72 Ligand excluded by PLIP BR.60: 4 residues within 4Å: Chain C: F.68, Q.69, R.79, G.81 Ligand excluded by PLIP BR.61: 3 residues within 4Å: Chain C: N.73, Q.74, S.75 Ligand excluded by PLIP BR.62: 3 residues within 4Å: Chain C: T.95, K.96, S.153 Ligand excluded by PLIP BR.63: 3 residues within 4Å: Chain C: S.99, N.100, K.141 Ligand excluded by PLIP BR.64: 2 residues within 4Å: Chain C: N.100, I.102 Ligand excluded by PLIP BR.65: 7 residues within 4Å: Chain B: Q.146, V.147, G.148 Chain C: P.123, D.124, V.125 Ligands: EDO.52 Ligand excluded by PLIP BR.66: 3 residues within 4Å: Chain C: Q.74, V.91, K.156 Ligand excluded by PLIP BR.67: 2 residues within 4Å: Chain B: A.36 Chain C: K.40 Ligand excluded by PLIP BR.68: 4 residues within 4Å: Chain A: N.119 Chain C: D.131, L.132, S.133 Ligand excluded by PLIP BR.69: 3 residues within 4Å: Chain A: K.60 Chain C: N.48 Ligands: BR.72 Ligand excluded by PLIP BR.70: 2 residues within 4Å: Chain C: L.105, A.106 Ligand excluded by PLIP BR.71: 3 residues within 4Å: Chain C: K.96, L.152, S.153 Ligand excluded by PLIP BR.72: 4 residues within 4Å: Chain A: K.60 Chain C: N.48 Ligands: BR.59, BR.69 Ligand excluded by PLIP BR.73: 3 residues within 4Å: Chain C: T.136, K.137 Ligands: BR.74 Ligand excluded by PLIP BR.74: 3 residues within 4Å: Chain C: K.137 Ligands: BR.73, BR.75 Ligand excluded by PLIP BR.75: 2 residues within 4Å: Chain C: K.137 Ligands: BR.74 Ligand excluded by PLIP

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

NA.22: 3 residues within 4Å: Chain A: T.32, T.34, T.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.32, A:T.34 NA.23: 3 residues within 4Å: Chain A: T.30, A.31, G.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.31 NA.24: 8 residues within 4Å: Chain A: G.116, N.117 Chain B: G.116, N.117 Chain C: G.116, N.117 Ligands: NA.51, NA.78 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:G.116, A:N.117, C:N.117, B:N.117 NA.49: 3 residues within 4Å: Chain B: T.32, T.34, T.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.32, B:T.34 NA.50: 3 residues within 4Å: Chain B: T.30, A.31, G.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.31 NA.51: 8 residues within 4Å: Chain A: G.116, N.117 Chain B: G.116, N.117 Chain C: G.116, N.117 Ligands: NA.24, NA.78 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:G.116, A:N.117, C:N.117, B:N.117 NA.76: 3 residues within 4Å: Chain C: T.32, T.34, T.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.32, C:T.32 NA.77: 3 residues within 4Å: Chain C: T.30, A.31, G.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.31 NA.78: 8 residues within 4Å: Chain A: G.116, N.117 Chain B: G.116, N.117 Chain C: G.116, N.117 Ligands: NA.24, NA.51 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:G.116, A:N.117, B:N.117, C:N.117

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

EDO.25: 8 residues within 4Å: Chain B: P.123, D.124, V.125, I.126, Q.146, V.147 Chain C: V.125 Ligands: BR.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.125, B:V.147 EDO.26: 6 residues within 4Å: Chain A: A.110, L.111, L.112, L.132 Chain B: Q.74, V.91 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.74, A:L.111 EDO.52: 8 residues within 4Å: Chain A: V.125 Chain C: P.123, D.124, V.125, I.126, Q.146, V.147 Ligands: BR.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.125, C:V.147 EDO.53: 6 residues within 4Å: Chain B: A.110, L.111, L.112, L.132 Chain C: Q.74, V.91 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.111, C:Q.74 EDO.79: 8 residues within 4Å: Chain A: P.123, D.124, V.125, I.126, Q.146, V.147 Chain B: V.125 Ligands: BR.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.125, A:V.147 EDO.80: 6 residues within 4Å: Chain A: Q.74, V.91 Chain C: A.110, L.111, L.112, L.132 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.74, C:L.111

3 x SO3: SULFITE ION(Non-covalent)

SO3.27: 11 residues within 4Å: Chain A: V.125, I.126, G.127 Chain B: V.125, I.126, G.127 Chain C: V.125, I.126, G.127 Ligands: SO3.54, SO3.81 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.126 SO3.54: 11 residues within 4Å: Chain A: V.125, I.126, G.127 Chain B: V.125, I.126, G.127 Chain C: V.125, I.126, G.127 Ligands: SO3.27, SO3.81 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.126 SO3.81: 11 residues within 4Å: Chain A: V.125, I.126, G.127 Chain B: V.125, I.126, G.127 Chain C: V.125, I.126, G.127 Ligands: SO3.27, SO3.54 1 PLIP interactions: 1 interactions with chain C Water bridges: C:I.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sycheva, L.V. et al., Crystal Structure of the putative tail fiber protein gp53 from the Acinetobacter baumannii bacteriophage AP22. Biorxiv (2019)

Release Date

2014-10-01

Peptides

Putative tail fiber protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative tail fiber protein