SMTL ID : 4tqg.1

Crystal structure of Megavirus UDP-GlcNAc 4,6-dehydratase, 5-epimerase Mg534

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.12, A:S.14, A:S.14, A:S.14, A:G.15, A:S.16, A:L.17, A:S.35, A:R.36, A:D.37, A:D.59, A:I.60, A:A.81, A:A.83, A:Y.140, A:Y.140, A:K.144, A:N.170, A:V.171, A:V.171 Water bridges: A:G.18 Salt bridges: A:R.36, A:K.40, A:K.85 pi-Stacking: A:Y.168 NDP.2: 27 residues within 4Å: Chain B: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.12, B:S.14, B:S.14, B:S.14, B:G.15, B:S.16, B:L.17, B:S.35, B:R.36, B:D.37, B:D.59, B:I.60, B:A.81, B:A.83, B:Y.140, B:Y.140, B:K.144, B:N.170, B:V.171, B:V.171 Water bridges: B:G.18 Salt bridges: B:R.36, B:K.40, B:K.85 pi-Stacking: B:Y.168 NDP.3: 27 residues within 4Å: Chain C: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.12, C:S.14, C:S.14, C:S.14, C:G.15, C:S.16, C:L.17, C:S.35, C:R.36, C:D.37, C:D.59, C:I.60, C:A.81, C:A.83, C:Y.140, C:Y.140, C:K.144, C:N.170, C:V.171, C:V.171 Water bridges: C:G.18 Salt bridges: C:R.36, C:K.40, C:K.85 pi-Stacking: C:Y.168 NDP.4: 27 residues within 4Å: Chain D: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.12, D:S.14, D:S.14, D:S.14, D:G.15, D:S.16, D:L.17, D:S.35, D:R.36, D:D.37, D:D.59, D:I.60, D:A.81, D:A.83, D:Y.140, D:K.144, D:Y.168, D:N.170, D:V.171, D:V.171 Water bridges: D:G.18 Salt bridges: D:R.36, D:K.40, D:K.85 pi-Stacking: D:Y.168 NDP.5: 27 residues within 4Å: Chain E: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain E Hydrogen bonds: E:G.12, E:S.14, E:S.14, E:S.14, E:G.15, E:S.16, E:L.17, E:S.35, E:R.36, E:D.37, E:D.59, E:I.60, E:A.81, E:A.83, E:Y.140, E:K.144, E:Y.168, E:N.170, E:V.171, E:V.171 Water bridges: E:G.18 Salt bridges: E:R.36, E:K.40, E:K.85 pi-Stacking: E:Y.168 NDP.6: 27 residues within 4Å: Chain F: G.12, G.13, S.14, G.15, S.16, L.17, S.35, R.36, D.37, K.40, G.58, D.59, I.60, A.81, A.82, A.83, K.85, T.100, V.128, S.129, T.130, Y.140, K.144, Y.168, G.169, N.170, V.171 25 PLIP interactions: 25 interactions with chain F Hydrogen bonds: F:G.12, F:S.14, F:S.14, F:S.14, F:G.15, F:S.16, F:L.17, F:S.35, F:R.36, F:D.37, F:D.59, F:I.60, F:A.81, F:A.83, F:Y.140, F:K.144, F:Y.168, F:N.170, F:V.171, F:V.171 Water bridges: F:G.18 Salt bridges: F:R.36, F:K.40, F:K.85 pi-Stacking: F:Y.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piacente, F. et al., Giant Virus Megavirus chilensis Encodes the Biosynthetic Pathway for Uncommon Acetamido Sugars. J.Biol.Chem. (2014)

Release Date

2014-06-25

Peptides

Putative dTDP-d-glucose 4 6-dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Putative dTDP-d-glucose 4 6-dehydratase