SMTL ID : 6k0h.1

Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: L.270, I.273, K.274, E.277, Y.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.274, A:E.277 Water bridges: A:K.274 PEG.2: 6 residues within 4Å: Chain A: H.250, I.251, K.253, F.257, Y.259, E.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.253 PEG.7: 5 residues within 4Å: Chain B: L.270, I.273, K.274, E.277, Y.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.274, B:E.277 Water bridges: B:K.274 PEG.8: 6 residues within 4Å: Chain B: H.250, I.251, K.253, F.257, Y.259, E.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.253

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 29 residues within 4Å: Chain A: G.8, A.10, G.11, F.12, I.13, D.32, N.33, Y.34, G.35, N.36, S.37, G.58, D.59, V.60, R.61, F.81, A.82, G.83, K.85, N.100, S.123, S.124, S.125, Y.150, K.154, Y.178, F.179, P.181 Ligands: UD1.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.178 Hydrogen bonds: A:G.8, A:F.12, A:I.13, A:N.33, A:N.33, A:Y.34, A:G.35, A:N.36, A:N.36, A:S.37, A:D.59, A:V.60, A:F.81, A:G.83, A:K.85, A:N.100, A:K.154, A:F.179 Water bridges: A:G.11, A:A.14, A:L.84, A:K.154 Salt bridges: A:K.85, A:K.85 NAD.9: 29 residues within 4Å: Chain B: G.8, A.10, G.11, F.12, I.13, D.32, N.33, Y.34, G.35, N.36, S.37, G.58, D.59, V.60, R.61, F.81, A.82, G.83, K.85, N.100, S.123, S.124, S.125, Y.150, K.154, Y.178, F.179, P.181 Ligands: UD1.10 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.178 Hydrogen bonds: B:G.8, B:F.12, B:I.13, B:N.33, B:N.33, B:Y.34, B:G.35, B:N.36, B:N.36, B:S.37, B:D.59, B:V.60, B:F.81, B:G.83, B:K.85, B:N.100, B:Y.150, B:K.154, B:F.179 Water bridges: B:G.11, B:A.14, B:L.84, B:K.154 Salt bridges: B:K.85, B:K.85

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.4: 22 residues within 4Å: Chain A: K.85, A.86, V.87, S.125, A.126, Y.150, Y.178, F.179, N.180, A.199, N.200, L.201, Q.217, V.218, Y.219, G.230, R.232, Y.234, V.269, R.292, D.295 Ligands: NAD.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:K.85, A:L.201, A:Y.219 Hydrogen bonds: A:K.85, A:K.85, A:Y.150, A:Y.150, A:Y.178, A:N.180, A:A.199, A:L.201, A:Q.217, A:Y.219, A:Y.219 Water bridges: A:N.200, A:T.202, A:Q.217, A:G.230, A:R.232, A:R.292, A:R.292, A:R.292, A:R.292, A:R.292, A:R.292, A:D.295 Salt bridges: A:R.232, A:R.292, A:R.292 UD1.10: 22 residues within 4Å: Chain B: K.85, A.86, V.87, S.125, A.126, Y.150, Y.178, F.179, N.180, A.199, N.200, L.201, Q.217, V.218, Y.219, G.230, R.232, Y.234, V.269, R.292, D.295 Ligands: NAD.9 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:K.85, B:L.201, B:Y.219 Hydrogen bonds: B:K.85, B:K.85, B:Y.150, B:Y.178, B:N.180, B:A.199, B:L.201, B:Q.217, B:Y.219, B:Y.219 Water bridges: B:N.200, B:T.202, B:Q.217, B:Y.219, B:G.230, B:R.292, B:R.292, B:R.292, B:R.292, B:R.292, B:R.292, B:D.295, B:D.295, B:D.295 Salt bridges: B:R.232, B:R.292, B:R.292

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: K.308 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.308, H2O.8 MG.6: 1 residues within 4Å: Chain A: G.266 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.266, H2O.1, H2O.7, H2O.7, H2O.9 MG.11: 1 residues within 4Å: Chain B: K.308 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.308, H2O.16 MG.12: 1 residues within 4Å: Chain B: G.266 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.266, H2O.10, H2O.15, H2O.15, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, Y.W. et al., Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep (2019)

Release Date

2019-08-07

Peptides

UDP-glucose 4-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-glucose 4-epimerase

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