SMTL ID : 7uk8.1

Apo form of YgiC from Escherichia coli K-12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: E.22, H.25 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.22, A:E.22, A:H.25

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

SO4.2: 3 residues within 4Å: Chain A: V.53, E.57, F.159 No protein-ligand interaction detected (PLIP) SO4.3: 3 residues within 4Å: Chain A: S.77, D.78, E.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.78, A:D.78, A:E.79 SO4.4: 3 residues within 4Å: Chain A: S.92, R.95, Q.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.92, A:Q.96 SO4.5: 3 residues within 4Å: Chain A: G.117, E.118, K.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.118, A:E.118 Salt bridges: A:K.120 SO4.6: 4 residues within 4Å: Chain A: Q.303, M.304, E.305, Q.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.305 SO4.7: 4 residues within 4Å: Chain A: D.376, R.377, S.385, R.386 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.376, A:R.377, A:S.385 Salt bridges: A:R.377, A:R.386 SO4.8: 6 residues within 4Å: Chain A: N.125, A.126, D.127, T.128, P.129, S.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.125, A:A.126, A:D.127, A:T.128

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 1 residues within 4Å: Chain A: D.258 No protein-ligand interaction detected (PLIP)

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 YgiC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative acid--amine ligase YgiC

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