SMTL ID : 7z15.1

E. coli C-P lyase bound to a PhnK/PhnL dual ABC dimer and ADP + Pi

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-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 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.328, C:H.333, H2O.12, H2O.12, H2O.20 ZN.2: 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.4: 6 residues within 4Å: Chain G: H.328, L.329, H.333 Chain H: R.107, H.108 Ligands: I9X.6 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:H.328, G:H.333, H2O.31, H2O.31, H2O.32 ZN.5: 6 residues within 4Å: Chain H: C.241, I.243, C.244, S.246, 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

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

I9X.3: 21 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, A.207, G.208, R.209 Ligands: ZN.1 18 PLIP interactions: 14 interactions with chain D, 4 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:Q.124, D:G.208, D:R.209 Water bridges: D:G.52, D:V.125, C:D.336 Salt bridges: D:R.107, D:H.108, C:H.328, C:H.328, C:H.333 I9X.6: 21 residues within 4Å: Chain G: F.325, H.328, L.331, H.333 Chain H: 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, A.207, G.208, R.209 Ligands: ZN.4 19 PLIP interactions: 15 interactions with chain H, 4 interactions with chain G Hydrogen bonds: H:G.47, H:W.48, H:G.49, H:T.50, H:T.50, H:G.51, H:R.107, H:Q.124, H:G.208, H:R.209 Water bridges: H:G.52, H:H.108, H:V.125, G:D.336 Salt bridges: H:R.107, H:H.108, G:H.328, G:H.328, G:H.333

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 17 residues within 4Å: Chain I: Y.15, K.19, G.20, S.40, G.41, S.42, G.43, K.44, T.45, T.46 Chain J: R.138, T.145, F.146, S.147, M.150 Ligands: PO4.8, MG.9 16 PLIP interactions: 4 interactions with chain J, 12 interactions with chain I Hydrogen bonds: J:R.138, J:R.138, J:S.147, I:G.41, I:S.42, I:S.42, I:G.43, I:K.44, I:T.45, I:T.45, I:T.46, I:T.46 Water bridges: J:G.148 Salt bridges: I:K.44 pi-Stacking: I:Y.15, I:Y.15 ADP.10: 17 residues within 4Å: Chain I: R.138, T.145, F.146, S.147, M.150 Chain J: Y.15, K.19, G.20, S.40, G.41, S.42, G.43, K.44, T.45, T.46 Ligands: PO4.11, MG.12 17 PLIP interactions: 13 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:G.41, J:S.42, J:S.42, J:G.43, J:K.44, J:T.45, J:T.45, J:T.46, J:T.46, I:R.138, I:R.138, I:S.147 Water bridges: J:Y.15, I:G.148 Salt bridges: J:K.44 pi-Stacking: J:Y.15, J:Y.15

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 14 residues within 4Å: Chain I: S.40, G.41, K.44, T.45, Q.90, E.171, H.204 Chain J: S.147, G.148, G.149, M.150, G.175 Ligands: ADP.7, MG.9 10 PLIP interactions: 2 interactions with chain J, 8 interactions with chain I Hydrogen bonds: J:G.148, J:G.149, I:S.40, I:S.40, I:G.41, I:Q.90, I:E.171 Water bridges: I:T.45 Salt bridges: I:K.44, I:H.204 PO4.11: 14 residues within 4Å: Chain I: S.147, G.148, G.149, M.150, G.175 Chain J: S.40, G.41, K.44, T.45, Q.90, E.171, H.204 Ligands: ADP.10, MG.12 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:S.40, J:S.40, J:G.41, J:Q.90, J:E.171, I:G.148, I:G.149 Water bridges: J:T.45 Salt bridges: J:K.44, J:H.204

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 8 residues within 4Å: Chain I: T.45, Q.90, D.170, E.171 Chain J: S.147, G.148 Ligands: ADP.7, PO4.8 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:T.45, H2O.40, H2O.40 MG.12: 8 residues within 4Å: Chain I: S.147, G.148 Chain J: T.45, Q.90, D.170, E.171 Ligands: ADP.10, PO4.11 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:T.45, H2O.42, H2O.43 MG.14: 2 residues within 4Å: Chain K: S.48 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain L: S.48 Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.13: 20 residues within 4Å: Chain I: D.235, D.236, P.237 Chain J: L.255 Chain K: F.11, L.13, L.21, V.23, H.42, S.43, G.44, S.45, G.46, K.47, S.48, T.49, Y.58, D.174, I.205 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.44, K:S.45, K:S.45, K:G.46, K:K.47, K:S.48, K:T.49, K:T.49, K:Y.58, K:Y.58, K:D.174 Salt bridges: K:K.47, K:K.47 pi-Stacking: K:F.11, K:F.11 ATP.15: 20 residues within 4Å: Chain I: L.255 Chain J: D.235, D.236, P.237 Chain L: F.11, L.13, L.21, V.23, H.42, S.43, G.44, S.45, G.46, K.47, S.48, T.49, Y.58, D.174, I.205 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.44, L:S.45, L:S.45, L:G.46, L:K.47, L:S.48, L:T.49, L:T.49, L:Y.58, L:Y.58, L:D.174 Salt bridges: L:K.47, L:K.47 pi-Stacking: L:F.11, L:F.11

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

2022-06-22

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
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL: KL

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

K
K

L
L

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

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

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