SMTL ID : 9dr4.1

Crystal structure of bifunctional GlmU from Staphylococcus aureus NCTC 8325 complexed with UTP, CoA and Glc 1-P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 13 residues within 4Å: Chain A: K.455, Y.458 Chain B: V.394, Y.396 Chain C: G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 15 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.429, C:A.431, B:V.394 Hydrogen bonds: C:C.414, C:A.432, C:R.449, C:R.449, C:R.449, C:R.451, B:Y.396 Water bridges: C:R.449, B:Y.396 pi-Cation interactions: C:R.451, C:R.451 Salt bridges: A:K.455 COA.5: 13 residues within 4Å: Chain A: G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 Chain B: K.455, Y.458 Chain C: V.394, Y.396 15 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:L.429, A:A.431, C:V.394 Hydrogen bonds: A:C.414, A:A.432, A:R.449, A:R.449, A:R.449, A:R.451, C:Y.396 Water bridges: A:R.449, C:Y.396 pi-Cation interactions: A:R.451, A:R.451 Salt bridges: B:K.455 COA.9: 13 residues within 4Å: Chain A: V.394, Y.396 Chain B: G.413, C.414, L.429, A.431, A.432, L.445, V.447, R.449, R.451 Chain C: K.455, Y.458 15 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:L.429, B:A.431, A:V.394 Hydrogen bonds: B:C.414, B:A.432, B:R.449, B:R.449, B:R.449, B:R.451, A:Y.396 Water bridges: B:R.449, A:Y.396 pi-Cation interactions: B:R.451, B:R.451 Salt bridges: C:K.455

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.415 Chain B: N.415 Chain C: N.415 Ligands: MG.6, MG.10 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: N.415 Chain B: N.415 Chain C: N.415 Ligands: MG.2, MG.10 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: N.415 Chain B: N.415 Chain C: N.415 Ligands: MG.2, MG.6 No protein-ligand interaction detected (PLIP)

3 x G1P: 1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G1P.3: 10 residues within 4Å: Chain B: R.342, K.360, Y.375, N.395, Y.396, K.401 Chain C: K.369, S.371, H.372, N.386 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Y.375, B:Y.375, B:N.395, B:N.395, C:S.371, C:H.372, C:N.386 Water bridges: B:N.395, B:K.401, B:K.401, C:S.371, C:N.386 Salt bridges: B:R.342, B:K.360, B:K.401, B:K.401 G1P.7: 10 residues within 4Å: Chain A: K.369, S.371, H.372, N.386 Chain C: R.342, K.360, Y.375, N.395, Y.396, K.401 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:Y.375, C:Y.375, C:N.395, C:N.395, A:S.371, A:H.372, A:N.386 Water bridges: C:N.395, C:K.401, C:K.401, A:S.371, A:N.386 Salt bridges: C:R.342, C:K.360, C:K.401, C:K.401 G1P.11: 10 residues within 4Å: Chain A: R.342, K.360, Y.375, N.395, Y.396, K.401 Chain B: K.369, S.371, H.372, N.386 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:S.371, B:H.372, B:N.386, A:Y.375, A:Y.375, A:N.395, A:N.395 Water bridges: B:S.371, B:N.386, A:N.395, A:K.401, A:K.401 Salt bridges: A:R.342, A:K.360, A:K.401, A:K.401

3 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.4: 18 residues within 4Å: Chain A: L.18, A.19, A.20, G.21, K.22, G.23, T.24, R.25, K.32, Q.82, Q.85, L.86, G.87, A.91, C.110, G.111, D.112, N.237 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.20, A:G.21, A:G.23, A:T.24, A:R.25, A:R.25, A:Q.82, A:Q.82, A:G.87, A:G.111, A:D.112, A:D.112, A:N.237 Water bridges: A:K.22, A:K.22, A:K.32, A:K.32, A:N.237, A:N.237 Salt bridges: A:R.25, A:K.32, A:K.32, A:K.32 UTP.8: 18 residues within 4Å: Chain B: L.18, A.19, A.20, G.21, K.22, G.23, T.24, R.25, K.32, Q.82, Q.85, L.86, G.87, A.91, C.110, G.111, D.112, N.237 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.20, B:G.21, B:G.23, B:T.24, B:R.25, B:R.25, B:Q.82, B:Q.82, B:G.87, B:G.111, B:D.112, B:D.112, B:N.237 Water bridges: B:K.22, B:K.22, B:K.32, B:K.32, B:N.237, B:N.237 Salt bridges: B:R.25, B:K.32, B:K.32, B:K.32 UTP.12: 18 residues within 4Å: Chain C: L.18, A.19, A.20, G.21, K.22, G.23, T.24, R.25, K.32, Q.82, Q.85, L.86, G.87, A.91, C.110, G.111, D.112, N.237 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:A.20, C:G.21, C:G.23, C:T.24, C:R.25, C:R.25, C:Q.82, C:Q.82, C:G.87, C:G.111, C:D.112, C:D.112, C:N.237 Water bridges: C:K.22, C:K.22, C:K.32, C:K.32, C:N.237, C:N.237 Salt bridges: C:R.25, C:K.32, C:K.32, C:K.32

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

Related Entries With Identical Sequence