SMTL ID : 4xb6.1

Structure of the E. coli C-P lyase core complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Q.85 Chain C: A.55, R.57, Y.229, E.247, L.248, L.249 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:L.249, C:L.249, A:Q.85 Water bridges: C:R.57, C:R.57 SO4.3: 10 residues within 4Å: Chain D: Y.46, G.47, W.48, G.49, T.50, G.51, G.52, A.207, G.208, R.209 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.47, D:W.48, D:G.49, D:T.50, D:T.50, D:G.51, D:V.125, D:G.208, D:R.209 Water bridges: D:R.209, D:E.210 SO4.5: 6 residues within 4Å: Chain E: Q.85 Chain G: R.57, Y.229, E.247, L.248, L.249 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:L.249 Water bridges: G:R.57, G:R.57, G:R.57, G:R.57 Salt bridges: G:R.57 SO4.7: 12 residues within 4Å: Chain H: Y.46, G.47, W.48, G.49, T.50, G.51, G.52, V.125, P.126, A.207, G.208, R.209 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:G.47, H:G.47, H:W.48, H:G.49, H:T.50, H:T.50, H:T.50, H:G.51, H:G.208, H:R.209 Water bridges: H:V.125, H:V.125, H:R.209

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain C: H.328, L.329, H.333 Chain D: R.107 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.328, C:H.333, H2O.17 ZN.4: 6 residues within 4Å: Chain D: C.241, I.243, C.244, S.246, C.266, C.272 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.241, D:C.244, D:C.266, D:C.272 ZN.6: 4 residues within 4Å: Chain G: H.328, L.329, H.333 Chain H: R.107 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.328, G:H.333, H2O.51 ZN.8: 5 residues within 4Å: Chain H: C.241, I.243, C.244, C.266, C.272 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.241, H:C.244, H:C.266, H:C.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seweryn, P. et al., Structural insights into the bacterial carbon-phosphorus lyase machinery. Nature (2015)

Release Date

2015-08-19

Peptides

Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG: AE
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH: BF
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI: CG
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG

Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH

Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI

Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase

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