SMTL ID : 3lu1.2 (1 other biounit)

Crystal Structure Analysis of WbgU: a UDP-GalNAc 4-epimerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 29 residues within 4Å: Chain A: G.45, A.47, G.48, F.49, I.50, D.69, N.70, F.71, S.72, T.73, G.74, G.99, D.100, I.101, R.102, Q.120, A.121, A.122, T.139, A.162, A.163, S.164, Y.188, K.192, Y.215, N.217, V.218, Q.223 Ligands: UD2.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.215 Hydrogen bonds: A:A.47, A:A.47, A:F.49, A:I.50, A:N.70, A:S.72, A:S.72, A:T.73, A:T.73, A:T.73, A:T.73, A:G.74, A:D.100, A:I.101, A:Q.120, A:A.122, A:K.192, A:V.218, A:Q.223 Water bridges: A:G.51 pi-Stacking: A:Y.215 NAD.4: 29 residues within 4Å: Chain B: G.45, A.47, G.48, F.49, I.50, D.69, N.70, F.71, S.72, T.73, G.74, G.99, D.100, I.101, R.102, Q.120, A.121, A.122, T.139, A.162, A.163, S.164, Y.188, K.192, Y.215, N.217, V.218, Q.223 Ligands: UD2.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.215 Hydrogen bonds: B:A.47, B:F.49, B:I.50, B:N.70, B:N.70, B:F.71, B:S.72, B:S.72, B:T.73, B:T.73, B:T.73, B:G.74, B:D.100, B:I.101, B:R.102, B:Q.120, B:A.122, B:Y.188, B:K.192, B:V.218, B:Q.223 Water bridges: B:G.48, B:G.51 pi-Stacking: B:Y.215

2 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.2: 24 residues within 4Å: Chain A: G.124, S.125, S.164, S.165, S.166, Y.188, Y.215, N.217, A.231, V.232, K.235, W.236, Y.247, I.248, N.249, T.254, R.256, L.293, R.318, R.321, D.324, V.325, S.328 Ligands: NAD.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.232, A:V.325 Hydrogen bonds: A:S.125, A:S.164, A:S.165, A:S.165, A:S.166, A:Y.188, A:N.217, A:N.217, A:N.217, A:V.232, A:K.235, A:Y.247, A:N.249, A:N.249, A:R.318, A:R.321, A:D.324 Water bridges: A:R.321, A:R.321, A:R.321, A:D.324 Salt bridges: A:R.256, A:R.321, A:R.321 UD2.5: 24 residues within 4Å: Chain B: G.124, S.125, V.126, S.164, S.165, S.166, Y.188, Y.215, N.217, A.231, V.232, K.235, W.236, Y.247, I.248, N.249, T.254, R.256, L.293, R.321, D.324, V.325, S.328 Ligands: NAD.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.232, B:V.325 Hydrogen bonds: B:S.125, B:S.164, B:S.165, B:S.165, B:N.217, B:N.217, B:N.217, B:N.217, B:V.232, B:K.235, B:Y.247, B:N.249, B:N.249, B:T.254, B:R.321, B:R.321, B:D.324 Salt bridges: B:R.256, B:R.321

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 3 residues within 4Å: Chain A: K.275, D.276, S.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.275, A:K.275, A:S.277, A:S.277 GLY.9: 2 residues within 4Å: Chain B: R.326, H.327 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.326, B:R.326

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

NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain B: R.26, K.275, K.340 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.26, B:K.275, B:K.340 SO4.8: 3 residues within 4Å: Chain B: H.75, Q.76, Y.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.76, B:Y.77 Salt bridges: B:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhatt, V.S. et al., Altered architecture of substrate binding region defines the unique specificity of UDP-GalNAc 4-epimerases. Protein Sci. (2011)

Release Date

2010-07-21

Peptides

WbgU: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

WbgU

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