SMTL ID : 5dld.2 (1 other biounit)

Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 18 residues within 4Å: Chain A: R.19, P.20, I.23, H.222, R.223, P.253, P.279, Q.280, Y.282, F.285, M.289, S.299, G.300, G.301, I.302, E.305 Ligands: UD1.2, ACT.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.19, A:Q.280, A:Q.280, A:S.299, A:G.300, A:G.301, A:E.305 Water bridges: A:Y.282, A:S.299, A:S.299 Salt bridges: A:R.19, A:H.222, A:H.222, A:R.223 pi-Stacking: A:F.285 pi-Cation interactions: A:R.19 UDP.9: 18 residues within 4Å: Chain B: R.19, P.20, I.23, H.222, R.223, P.253, P.279, Q.280, Y.282, F.285, M.289, S.299, G.300, G.301, I.302, E.305 Ligands: UD1.10, ACT.13 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.19, B:Q.280, B:Q.280, B:S.299, B:G.300, B:G.301, B:E.305 Water bridges: B:Y.282, B:S.299, B:S.299 Salt bridges: B:R.19, B:H.222, B:H.222, B:R.223 pi-Stacking: B:F.285 pi-Cation interactions: B:R.19

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

UD1.2: 24 residues within 4Å: Chain A: P.20, Q.47, H.48, R.49, Q.50, M.51, M.70, R.71, Q.72, G.73, Q.74, L.76, T.105, T.106, P.139, E.140, H.222, R.223, R.224, H.255, L.256, N.257, P.258 Ligands: UDP.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:H.48, A:L.76, A:P.139 Hydrogen bonds: A:Q.47, A:R.49, A:M.51, A:R.71, A:G.73, A:Q.74, A:Q.74, A:T.106, A:E.140, A:E.140, A:R.223, A:R.224, A:N.257 Water bridges: A:E.140, A:R.224, A:R.224, A:L.256 Salt bridges: A:H.48, A:H.48, A:H.48, A:R.224, A:R.224, A:H.255, A:H.255 UD1.10: 24 residues within 4Å: Chain B: P.20, Q.47, H.48, R.49, Q.50, M.51, M.70, R.71, Q.72, G.73, Q.74, L.76, T.105, T.106, P.139, E.140, H.222, R.223, R.224, H.255, L.256, N.257, P.258 Ligands: UDP.9 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:H.48, B:L.76, B:P.139 Hydrogen bonds: B:Q.47, B:R.49, B:M.51, B:R.71, B:G.73, B:Q.74, B:Q.74, B:T.106, B:T.106, B:E.140, B:R.223, B:R.224, B:N.257 Water bridges: B:E.140, B:R.224, B:R.224, B:L.256 Salt bridges: B:H.48, B:H.48, B:H.48, B:R.224, B:R.224, B:H.255, B:H.255

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: T.220, G.221, H.222, F.231, F.234, D.298, T.316 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.223, A:D.298, A:T.316, A:T.316 Water bridges: A:S.226, A:S.226 EDO.11: 7 residues within 4Å: Chain B: T.220, G.221, H.222, F.231, F.234, D.298, T.316 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.223, B:D.298, B:T.316 Water bridges: B:S.226, B:S.226

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

ACT.4: 4 residues within 4Å: Chain A: F.209, Q.249, A.272, Y.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.209, A:Q.249 Water bridges: A:Y.275 ACT.5: 8 residues within 4Å: Chain A: D.104, P.137, R.144, R.223, G.300, E.321, R.322 Ligands: UDP.1 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.322 Salt bridges: A:R.144, A:R.223, A:R.317, A:R.322 ACT.6: 6 residues within 4Å: Chain A: R.317, D.318, L.333, V.334, G.335, L.340 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.340 Hydrogen bonds: A:D.318, A:L.333 Water bridges: A:T.336 ACT.12: 4 residues within 4Å: Chain B: F.209, Q.249, A.272, Y.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.209, B:Q.249, B:Y.275 ACT.13: 8 residues within 4Å: Chain B: D.104, P.137, R.144, R.223, G.300, E.321, R.322 Ligands: UDP.9 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.322 Salt bridges: B:R.144, B:R.223, B:R.317, B:R.322 ACT.14: 6 residues within 4Å: Chain B: R.317, D.318, L.333, V.334, G.335, L.340 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.340 Hydrogen bonds: B:L.333 Water bridges: B:T.336

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: K.33, R.35, V.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.32 NA.15: 3 residues within 4Å: Chain B: K.33, R.35, V.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.38

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: Y.119 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.119 GOL.16: 1 residues within 4Å: Chain B: Y.119 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP. to be published

Release Date

2015-09-30

Peptides

UDP-N-Acetylglucosamine 2-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-N-Acetylglucosamine 2-epimerase

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