SMTL ID : 5dip.1

Crystal structure of lpg0406 in reduced form from Legionella pneumophila

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: C.72, H.76 Chain B: Y.99, M.100 Chain E: G.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.76 NA.2: 5 residues within 4Å: Chain A: M.31, P.32, E.33, L.34 Chain F: K.47 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:E.33, A:L.34, F:K.47, F:K.47 NA.4: 4 residues within 4Å: Chain A: M.100 Chain B: C.72, H.76 Chain D: G.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.99 NA.5: 5 residues within 4Å: Chain A: G.103 Chain C: C.72, H.76 Chain D: Y.99, M.100 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.76 Water bridges: D:Y.99 NA.6: 5 residues within 4Å: Chain B: K.47 Chain C: M.31, P.32, E.33, L.34 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:M.31, C:E.33, C:L.34, B:K.47 NA.8: 4 residues within 4Å: Chain C: M.100 Chain D: C.72, H.76 Chain F: G.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.99 NA.9: 5 residues within 4Å: Chain C: G.103 Chain E: C.72, H.76 Chain F: Y.99, M.100 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.99 NA.10: 5 residues within 4Å: Chain D: K.47 Chain E: M.31, P.32, E.33, L.34 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:M.31, E:E.33, E:L.34, D:K.47 NA.12: 4 residues within 4Å: Chain B: G.103 Chain E: M.100 Chain F: C.72, H.76 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:Y.99 Hydrogen bonds: F:H.76

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain B: K.12, A.110, E.111, E.114 Chain F: I.16, D.19, I.20, Q.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.12, B:A.110, B:E.114 GOL.7: 8 residues within 4Å: Chain B: I.16, D.19, I.20, Q.23 Chain D: K.12, A.110, E.111, E.114 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.12, D:A.110, D:E.114 GOL.11: 8 residues within 4Å: Chain D: I.16, D.19, I.20, Q.23 Chain F: K.12, A.110, E.111, E.114 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.12, F:A.110, F:E.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila. Protein Sci. (2015)

Release Date

2015-10-14

Peptides

Alkyl hydroperoxide reductase AhpD: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Alkyl hydroperoxide reductase AhpD

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