SMTL ID : 7k3p.1

The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 32 residues within 4Å: Chain A: G.23, A.25, G.26, Y.27, I.28, L.46, D.47, N.48, L.49, S.50, K.51, G.52, Q.71, D.72, L.73, F.94, A.95, A.96, I.98, N.113, N.117, S.136, S.137, Y.162, K.166, Y.190, F.191, N.192, V.193, A.196, M.198 Ligands: GOL.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.190, A:V.193 Hydrogen bonds: A:A.25, A:Y.27, A:I.28, A:N.48, A:L.49, A:S.50, A:S.50, A:K.51, A:G.52, A:L.73, A:F.94, A:A.96, A:N.113, A:N.113, A:N.117, A:K.166, A:N.192, A:V.193, A:V.193 Water bridges: A:G.29, A:S.74 NAD.6: 32 residues within 4Å: Chain B: G.23, A.25, G.26, Y.27, I.28, L.46, D.47, N.48, L.49, S.50, K.51, G.52, Q.71, D.72, L.73, F.94, A.95, A.96, I.98, N.113, N.117, S.136, S.137, Y.162, K.166, Y.190, F.191, N.192, V.193, A.196 Ligands: GOL.7, GOL.10 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.190, B:V.193 Hydrogen bonds: B:A.25, B:Y.27, B:I.28, B:N.48, B:L.49, B:S.50, B:K.51, B:G.52, B:L.73, B:F.94, B:A.96, B:N.113, B:N.113, B:N.117, B:S.136, B:K.166, B:Y.190, B:V.193 Water bridges: B:G.29, B:S.50, B:K.51, B:K.51, B:S.74 Salt bridges: B:K.51, B:K.51

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.31, D.249, S.336, W.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.31 GOL.3: 5 residues within 4Å: Chain A: M.168, E.171 Chain B: L.167, M.168, E.171 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.171, B:L.167 GOL.4: 6 residues within 4Å: Chain A: N.48, S.50, D.72, K.109, N.113 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.48, A:S.50, A:D.72, A:K.109 Water bridges: A:K.109 GOL.7: 8 residues within 4Å: Chain B: I.98, T.138, A.139, Y.162, Y.190, F.191, N.192 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.98, B:T.138, B:T.138, B:A.139, B:Y.162 GOL.8: 8 residues within 4Å: Chain B: Y.206, P.207, K.208, L.212, L.227, F.228, F.230, R.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.206, B:F.228, B:R.303 GOL.9: 4 residues within 4Å: Chain B: R.318, W.323, Q.324, P.325 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.323 Water bridges: B:R.318 GOL.10: 5 residues within 4Å: Chain B: N.48, S.50, K.109, N.113 Ligands: NAD.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.48, B:S.50, B:D.72, B:K.109 Water bridges: B:S.97, B:K.109

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

ACT.5: 7 residues within 4Å: Chain A: K.208, A.209, T.210, R.243, D.306, P.307, L.310 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.208 Hydrogen bonds: A:A.209, A:T.210, A:T.210 Salt bridges: A:K.208, A:R.243 ACT.11: 6 residues within 4Å: Chain B: K.208, A.209, T.210, R.243, P.307, L.310 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.208, B:A.209, B:T.210 Hydrogen bonds: B:T.210 Water bridges: B:A.209 Salt bridges: B:K.208, B:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, H.G. et al., The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen

Release Date

2021-09-29

Peptides

UDP-glucose 4-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-glucose 4-epimerase