SMTL ID : 7w1g.3 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x 87E: (2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid(Non-covalent)

87E.1: 22 residues within 4Å: Chain A: Q.69, H.71, M.103, T.104, A.105, D.106, A.107, H.124, G.126, W.127, R.128, I.157, F.162, E.163, V.164, G.165, E.167, V.168, K.189, Y.227, R.228, R.235 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.157, A:F.162, A:Y.227 Hydrogen bonds: A:Q.69, A:H.71, A:A.105, A:A.107, A:W.127, A:R.128, A:E.163, A:G.165, A:K.189, A:R.228, A:R.228 Water bridges: A:H.71, A:R.128, A:R.128, A:R.228 Salt bridges: A:R.128, A:R.128, A:R.228, A:R.235 pi-Cation interactions: A:R.228

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Chain A: R.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53

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
C

Purine nucleoside phosphorylase YfiH

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