SMTL ID : 9dqf.1

Crystal structure of bifunctional GlmU from Staphylococcus aureus NCTC 8325 complexed with acetyl CoA and citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 23 residues within 4Å: Chain A: K.455, Y.458 Chain B: H.372, G.388, C.389, F.411, G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 Chain C: Y.375, I.392, T.393, V.394, N.395, Y.396, V.419 Ligands: CIT.2 23 PLIP interactions: 4 interactions with chain C, 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:Y.375, C:I.392, C:V.394, B:F.411, B:L.429, B:A.431 Hydrogen bonds: C:Y.396, B:C.389, B:C.414, B:A.432, B:R.449, B:R.449, B:R.449, B:R.451, B:R.451, A:Y.458, A:Y.458 Water bridges: B:R.449, A:K.455, A:K.455 pi-Cation interactions: B:R.451, B:R.451 Salt bridges: A:K.455 ACO.3: 23 residues within 4Å: Chain A: Y.375, I.392, T.393, V.394, N.395, Y.396, V.419 Chain B: K.455, Y.458 Chain C: H.372, G.388, C.389, F.411, G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 Ligands: CIT.4 23 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 14 interactions with chain C Hydrogen bonds: B:Y.458, B:Y.458, A:Y.396, C:C.389, C:C.414, C:A.432, C:R.449, C:R.449, C:R.449, C:R.451, C:R.451 Water bridges: B:K.455, B:K.455, C:R.449 Salt bridges: B:K.455 Hydrophobic interactions: A:Y.375, A:I.392, A:V.394, C:F.411, C:L.429, C:A.431 pi-Cation interactions: C:R.451, C:R.451 ACO.5: 23 residues within 4Å: Chain A: H.372, G.388, C.389, F.411, G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 Chain B: Y.375, I.392, T.393, V.394, N.395, Y.396, V.419 Chain C: K.455, Y.458 Ligands: CIT.6 23 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:Y.375, B:I.392, B:V.394, A:F.411, A:L.429, A:A.431 Hydrogen bonds: B:Y.396, A:C.389, A:C.414, A:A.432, A:R.449, A:R.449, A:R.449, A:R.451, A:R.451, C:Y.458, C:Y.458 Water bridges: A:R.449, C:K.455, C:K.455 pi-Cation interactions: A:R.451, A:R.451 Salt bridges: C:K.455

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 9 residues within 4Å: Chain B: S.371, H.372 Chain C: R.342, K.360, Y.375, N.395, Y.396, K.401 Ligands: ACO.1 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Y.375, C:N.395, C:K.401, B:S.371, B:S.371 Salt bridges: C:R.342, C:R.342, C:K.360, C:K.401, C:K.401, B:H.372 Water bridges: B:S.371 CIT.4: 9 residues within 4Å: Chain A: R.342, K.360, Y.375, N.395, Y.396, K.401 Chain C: S.371, H.372 Ligands: ACO.3 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Y.375, A:N.395, A:K.401, C:S.371, C:S.371 Salt bridges: A:R.342, A:R.342, A:K.360, A:K.401, A:K.401, C:H.372 Water bridges: C:S.371 CIT.6: 9 residues within 4Å: Chain A: S.371, H.372 Chain B: R.342, K.360, Y.375, N.395, Y.396, K.401 Ligands: ACO.5 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.375, B:N.395, B:K.401, A:S.371, A:S.371 Salt bridges: B:R.342, B:R.342, B:K.360, B:K.401, B:K.401, A:H.372 Water bridges: A:S.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pederick, J.L. et al., Functional and structural characterization of Staphylococcus aureus N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) reveals a redox-sensitive acetyltransferase activity. Protein Sci. (2025)

Release Date

2025-05-14

Peptides

Bifunctional protein GlmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein GlmU

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