SMTL ID : 4xi1.4 (3 other biounits)

Crystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legionella pneumophila str. Paris, wild-type

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: Q.86 Chain B: L.83, Q.86 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: Q.86 Chain F: Q.86 Ligands: CL.15 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain D: Q.86 Chain E: L.83, Q.86 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: Q.86 Chain F: Q.86 Ligands: CL.7 Ligand excluded by PLIP

10 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.2: 10 residues within 4Å: Chain A: V.78, V.79, F.80, D.81 Chain B: I.28, F.29, Q.86 Chain C: V.89, F.92, Y.93 8 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:Q.86, A:D.81, A:D.81 Hydrophobic interactions: C:V.89, C:F.92, C:F.92, C:F.92, A:V.78 HEZ.3: 6 residues within 4Å: Chain B: Y.90, Y.93, R.96, E.97 Chain C: Y.93, R.96 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.93 Hydrogen bonds: C:R.96, B:Y.90, B:R.96 HEZ.4: 11 residues within 4Å: Chain A: F.29, Q.86 Chain B: I.43, V.78, V.79, F.80, D.81, E.82 Chain D: Q.85, F.92, Y.93 10 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:I.43, B:F.80, D:F.92, D:F.92 Hydrogen bonds: B:D.81, B:D.81, B:D.81, A:Q.86, D:Q.85 Water bridges: B:E.82 HEZ.6: 9 residues within 4Å: Chain B: Q.85, V.89, F.92, Y.93 Chain C: F.29, Q.86 Chain F: V.79, F.80, D.81 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: B:F.92, B:F.92, F:F.80 Hydrogen bonds: B:Q.85, F:D.81, C:Q.86 HEZ.8: 11 residues within 4Å: Chain C: D.27, I.28, G.47, K.48, V.49 Chain F: D.27, I.28, G.47, K.48, V.49 Ligands: HEZ.16 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:I.28 Hydrogen bonds: C:G.47, C:V.49, F:V.49, F:V.49 HEZ.10: 10 residues within 4Å: Chain D: V.78, V.79, F.80, D.81 Chain E: I.28, F.29, Q.86 Chain F: V.89, F.92, Y.93 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: F:V.89, F:F.92, F:F.92, F:F.92, D:V.78 Hydrogen bonds: D:D.81, D:D.81, D:D.81, E:Q.86 HEZ.11: 6 residues within 4Å: Chain E: Y.90, Y.93, R.96, E.97 Chain F: Y.93, R.96 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:Y.93 Hydrogen bonds: F:R.96, E:Y.90, E:Y.90, E:R.96 HEZ.12: 11 residues within 4Å: Chain A: Q.85, F.92, Y.93 Chain D: F.29, Q.86 Chain E: I.43, V.78, V.79, F.80, D.81, E.82 9 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A, 4 interactions with chain E Hydrogen bonds: D:Q.86, A:Q.85, A:Y.93, E:D.81, E:D.81 Hydrophobic interactions: A:F.92, A:F.92, E:I.43, E:F.80 HEZ.14: 9 residues within 4Å: Chain C: V.79, F.80, D.81 Chain E: Q.85, V.89, F.92, Y.93 Chain F: F.29, Q.86 8 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: E:F.92, E:F.92, C:F.80 Hydrogen bonds: E:Q.85, E:Y.93, F:Q.86, C:D.81, C:D.81 HEZ.16: 11 residues within 4Å: Chain C: D.27, I.28, G.47, K.48, V.49 Chain F: D.27, I.28, G.47, K.48, V.49 Ligands: HEZ.8 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:V.49, C:V.49, F:G.47, F:V.49 Hydrophobic interactions: F:I.28

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: R.94, K.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.94, B:K.95, B:K.95 GOL.13: 2 residues within 4Å: Chain E: R.94, K.95 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.94, E:K.95, E:K.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quaile, A.T. et al., Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila. Structure (2015)

Release Date

2015-01-21

Peptides

E3 ubiquitin-protein ligase LubX: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

E3 ubiquitin-protein ligase LubX

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