SMTL ID : 5xvs.1

Crystal structure of UDP-GlcNAc 2-epimerase NeuC complexed with UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

2 x LI: LITHIUM ION(Non-covalent)

LI.1: 5 residues within 4Å: Chain A: I.24, Q.25, Q.26, D.27, L.30 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.24, A:Q.25, A:D.27, A:L.30, H2O.4 LI.3: 4 residues within 4Å: Chain B: I.24, Q.25, D.27, L.30 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.24, B:Q.25, B:D.27, B:L.30, H2O.14

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

UDP.2: 14 residues within 4Å: Chain A: T.208, H.210, S.238, S.269, F.270, G.271, I.272, Y.275, S.289, S.290, S.291, E.295, R.309, Q.310 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:F.270, A:G.271, A:S.290, A:S.290, A:S.290, A:S.291, A:E.295, A:Q.310 Water bridges: A:R.11 Salt bridges: A:H.210, A:H.210, A:R.309 pi-Stacking: A:Y.275 UDP.4: 15 residues within 4Å: Chain B: R.11, A.12, L.16, T.208, H.210, S.238, F.270, I.272, Y.275, S.289, S.290, S.291, E.295, R.309 Ligands: NAG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.11, B:N.241, B:F.270, B:F.270, B:S.290, B:S.290 Water bridges: B:T.10, B:G.15, B:S.294, B:R.309, B:Q.310, B:Q.310 Salt bridges: B:R.11, B:H.210, B:H.210, B:R.309 pi-Stacking: B:Y.275

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.5: 12 residues within 4Å: Chain B: A.12, E.13, L.16, L.101, G.102, D.103, H.125, E.128, R.139, S.290, R.313 Ligands: UDP.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:E.13, B:L.16, B:L.101 Hydrogen bonds: B:H.125, B:R.139, B:S.290, B:S.290, B:R.313 Water bridges: B:E.13, B:D.103, B:D.103, B:D.135, B:R.139, B:S.290, B:S.290, B:S.294, B:S.294, B:R.313 Salt bridges: B:R.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ko, T.P. et al., The tetrameric structure of sialic acid-synthesizing UDP-GlcNAc 2-epimerase fromAcinetobacter baumannii: A comparative study with human GNE. J. Biol. Chem. (2018)

Release Date

2018-04-11

Peptides

GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (Hydrolyzing)