SMTL ID : 7z17.1

E. coli C-P lyase bound to a PhnK ABC dimer in an open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain C: H.328, L.329, H.333 Chain D: R.107, H.108 Ligands: I9X.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.328, C:H.333 ZN.2: 7 residues within 4Å: Chain D: C.241, I.243, C.244, S.246, S.249, 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.4: 4 residues within 4Å: Chain C: H.219 Chain G: M.1, H.328, H.333 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Metal complexes: G:H.328, G:H.333, C:H.219 ZN.5: 6 residues within 4Å: Chain H: C.241, I.243, C.244, C.266, C.272, Q.275 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.241, H:C.244, H:C.266, H:C.272

1 x I9X: alpha-D-ribose-1,2-cyclic-phosphate-5-phosphate(Non-covalent)

I9X.3: 23 residues within 4Å: Chain C: F.325, H.328, L.331, H.333 Chain D: Y.46, G.47, W.48, G.49, T.50, G.51, G.52, R.107, H.108, Q.124, V.125, P.126, P.187, G.206, A.207, G.208, R.209, E.210 Ligands: ZN.1 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.47, D:W.48, D:G.49, D:T.50, D:T.50, D:G.51, D:R.107, D:G.208, D:R.209 Salt bridges: D:R.107, D:H.108, C:H.328, C:H.328, C:H.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amstrup, S.K. et al., Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase. Nat Commun (2023)

Release Date

2022-05-25

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
Putative phosphonates utilization ATP-binding protein PhnK: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

I
I

J
J

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

Putative phosphonates utilization ATP-binding protein PhnK

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