SMTL ID : 4nes.1

Crystal structure of Methanocaldococcus jannaschii UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

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

UD1.1: 20 residues within 4Å: Chain A: T.9, P.11, Q.37, H.38, Y.39, S.40, M.43, S.64, H.67, Q.70, T.96, N.97, E.129, H.207, R.208, H.241, P.242, R.243, K.246 Ligands: UDP.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:Q.37, A:Y.39, A:S.40, A:S.40, A:S.40, A:S.64, A:S.64, A:Q.70, A:N.97, A:E.129, A:E.129, A:R.208, A:K.246 Water bridges: A:Q.37, A:Y.39, A:R.243, A:R.243, A:R.243 Salt bridges: A:H.38, A:H.38, A:H.241, A:H.241, A:R.243, A:R.243 UD1.3: 20 residues within 4Å: Chain B: T.9, P.11, Q.37, H.38, Y.39, S.40, M.43, S.64, H.67, Q.70, T.96, N.97, E.129, H.207, R.208, H.241, P.242, R.243, K.246 Ligands: UDP.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.39 Hydrogen bonds: B:Q.37, B:Y.39, B:Y.39, B:S.40, B:S.40, B:S.40, B:S.64, B:S.64, B:Q.70, B:N.97, B:E.129, B:E.129, B:E.129, B:R.208, B:K.246 Water bridges: B:Q.37, B:Y.39, B:R.243, B:R.243, B:R.243 Salt bridges: B:H.38, B:H.38, B:H.241, B:H.241, B:R.243, B:R.243

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

UDP.2: 17 residues within 4Å: Chain A: R.10, P.11, I.14, F.47, H.207, R.208, S.239, P.268, V.269, G.270, Y.271, F.274, S.288, G.289, G.290, E.294 Ligands: UD1.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.10, A:S.239, A:V.269, A:V.269, A:S.288, A:G.289, A:G.290, A:E.294 Water bridges: A:R.10, A:D.95, A:R.208, A:S.288, A:S.288 Salt bridges: A:R.10, A:H.207, A:H.207, A:R.208 pi-Stacking: A:F.274 pi-Cation interactions: A:R.10 UDP.4: 17 residues within 4Å: Chain B: R.10, P.11, I.14, F.47, H.207, R.208, S.239, P.268, V.269, G.270, Y.271, F.274, S.288, G.289, G.290, E.294 Ligands: UD1.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.10, B:S.239, B:V.269, B:V.269, B:S.288, B:G.289, B:G.290, B:E.294 Water bridges: B:R.10, B:D.95, B:R.208, B:S.288, B:S.288 Salt bridges: B:R.10, B:H.207, B:H.207, B:R.208 pi-Stacking: B:F.274 pi-Cation interactions: B:R.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S.C. et al., Crystal structures of the archaeal UDP-GlcNAc 2-epimerase from Methanocaldococcus jannaschii reveal a conformational change induced by UDP-GlcNAc. Proteins (2014)

Release Date

2014-04-23

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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