SMTL ID : 7uk7.1

YjfC from Escherichia coli K-12 in complex with ADP, Mg2+ and SO4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

ADP.1: 25 residues within 4Å: Chain A: D.110, L.122, E.123, K.272, L.289, V.307, K.309, S.313, R.314, E.315, G.316, G.317, V.319, Q.344, A.345, F.346, Q.347, L.349, L.358, L.379, I.380, T.381 Ligands: MG.2, MG.3, SO4.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.123, A:K.309, A:E.315, A:G.316, A:G.317, A:A.345, A:Q.347, A:T.381, A:T.381, A:T.381 Water bridges: A:K.272, A:S.313, A:R.374, A:R.374 Salt bridges: A:K.272, A:K.272, A:K.309

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.123, N.125, K.272 Ligands: ADP.1, MG.3, SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.123, A:E.123, H2O.3 MG.3: 6 residues within 4Å: Chain A: D.110, E.123, N.125 Ligands: ADP.1, MG.2, SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.110, A:E.123, H2O.8

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

SO4.4: 6 residues within 4Å: Chain A: R.10, R.43, F.352, G.353, D.354, S.355 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.354, A:S.355, A:S.355 Water bridges: A:R.43, A:R.43 Salt bridges: A:R.10, A:R.43 SO4.5: 10 residues within 4Å: Chain A: R.108, D.110, E.123, N.125, R.314, E.315, R.374 Ligands: ADP.1, MG.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.123, A:N.125, A:E.315 Water bridges: A:R.374, A:R.374, A:R.374 Salt bridges: A:R.108, A:R.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pederick, J.L. et al., Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity. Biochemistry (2023)

Release Date

2023-02-15

Peptides

Putative acid--amine ligase YjfC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative acid--amine ligase YjfC

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