SMTL ID : 4zht.1 (1 other biounit)

Crystal structure of UDP-GlcNAc 2-epimerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-tetramer

Ligands

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

UDP.1: 18 residues within 4Å: Chain A: R.19, A.20, S.23, K.24, R.113, L.218, H.220, L.250, N.253, H.281, V.282, F.284, F.287, S.301, S.302, C.303, E.307, R.321 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.23, A:N.253, A:V.282, A:V.282, A:S.302, A:S.302, A:E.307 Water bridges: A:K.24, A:S.302 Salt bridges: A:R.19, A:R.113, A:H.220, A:H.220, A:R.321 pi-Stacking: A:F.287 UDP.3: 17 residues within 4Å: Chain B: R.19, A.20, S.23, K.24, R.113, L.218, H.220, L.250, N.253, H.281, V.282, F.284, F.287, S.301, S.302, E.307, R.321 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.23, B:N.253, B:V.282, B:V.282, B:S.301, B:S.302, B:E.307 Salt bridges: B:R.19, B:R.113, B:H.220, B:H.220, B:R.321 pi-Stacking: B:F.287 UDP.5: 18 residues within 4Å: Chain C: R.19, A.20, S.23, K.24, R.113, L.218, H.220, L.250, N.253, H.281, V.282, F.284, F.287, S.301, S.302, C.303, E.307, R.321 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.23, C:N.253, C:H.281, C:V.282, C:V.282, C:S.302, C:S.302, C:E.307 Water bridges: C:K.24, C:S.302 Salt bridges: C:R.19, C:R.113, C:H.220, C:H.220, C:R.321 pi-Stacking: C:F.287 UDP.7: 17 residues within 4Å: Chain D: R.19, A.20, S.23, K.24, R.113, L.218, H.220, L.250, N.253, H.281, V.282, F.284, F.287, S.301, S.302, E.307, R.321 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.23, D:N.253, D:H.281, D:V.282, D:V.282, D:S.301, D:S.302, D:E.307 Salt bridges: D:R.19, D:R.113, D:H.220, D:H.220, D:R.321 pi-Stacking: D:F.287

4 x NCC: CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID(Non-covalent)

NCC.2: 14 residues within 4Å: Chain A: D.53, F.251, K.259, V.262, R.266, E.271, A.278, V.279, K.280, H.281 Chain D: R.263, R.266, K.267 Ligands: NCC.8 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:F.251, A:V.262 Hydrogen bonds: A:K.259, A:R.266, A:K.280, A:K.280, A:H.281, A:H.281, D:R.263 Water bridges: A:E.271 Salt bridges: A:K.280, D:R.263, D:R.266, D:R.266, D:K.267 NCC.4: 14 residues within 4Å: Chain B: D.53, F.251, K.259, V.262, R.266, E.271, A.278, V.279, K.280, H.281 Chain C: R.263, R.266, K.267 Ligands: NCC.6 20 PLIP interactions: 7 interactions with chain C, 13 interactions with chain B Water bridges: C:R.263, C:R.266, B:D.53, B:S.258, B:K.280 Salt bridges: C:R.263, C:R.263, C:R.266, C:R.266, C:K.267, B:K.280 Hydrophobic interactions: B:F.251, B:V.262 Hydrogen bonds: B:K.259, B:R.266, B:K.280, B:K.280, B:H.281, B:H.281 pi-Stacking: B:F.251 NCC.6: 14 residues within 4Å: Chain B: R.263, R.266, K.267 Chain C: D.53, F.251, K.259, V.262, R.266, E.271, A.278, V.279, K.280, H.281 Ligands: NCC.4 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.251, C:V.262 Hydrogen bonds: C:K.259, C:R.266, C:K.280, C:K.280, C:H.281, C:H.281, B:R.263 Salt bridges: C:K.280, B:R.263, B:R.266, B:R.266, B:K.267 NCC.8: 14 residues within 4Å: Chain A: R.263, R.266, K.267 Chain D: D.53, F.251, K.259, V.262, R.266, E.271, A.278, V.279, K.280, H.281 Ligands: NCC.2 20 PLIP interactions: 13 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:F.251, D:V.262 Hydrogen bonds: D:K.259, D:R.266, D:K.280, D:K.280, D:H.281, D:H.281 Water bridges: D:D.53, D:S.258, D:K.280, A:R.263, A:R.266 Salt bridges: D:K.280, A:R.263, A:R.263, A:R.266, A:R.266, A:K.267 pi-Stacking: D:F.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S.C. et al., Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis. Sci Rep (2016)

Release Date

2016-06-01

Peptides

Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase

Related Entries With Identical Sequence