SMTL ID : 7f3v.2 (3 other biounits)

Crystal structure of YfiH with C107A mutation in complex with endogenous UDP-MurNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x EPZ: (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid(Non-covalent)

EPZ.1: 20 residues within 4Å: Chain A: H.71, T.104, A.105, D.106, A.107, H.124, G.126, W.127, R.128, F.162, E.163, V.164, G.165, E.167, V.168, K.189, Y.227, R.228, R.235 Ligands: PO4.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:D.106, A:F.162, A:Y.227 Hydrogen bonds: A:A.105, A:A.105, A:A.107, A:W.127, A:R.128, A:R.128, A:E.163, A:G.165, A:K.189, A:R.228, A:R.228 Water bridges: A:Q.69, A:R.128, A:Y.227, A:R.228 Salt bridges: A:H.71, A:H.124, A:R.128, A:R.128, A:R.228 pi-Cation interactions: A:R.228

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

PO4.2: 3 residues within 4Å: Chain A: H.71, R.235 Ligands: EPZ.1 6 PLIP interactions: 6 interactions with chain A Water bridges: A:H.71, A:H.124, A:H.124, A:R.235 Salt bridges: A:H.71, A:R.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M.S. et al., Structural Basis for the Peptidoglycan-Editing Activity of YfiH. Mbio (2021)

Release Date

2021-12-29

Peptides

Purine nucleoside phosphorylase YfiH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Purine nucleoside phosphorylase YfiH

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