SMTL ID : 3ru7.1 (1 other biounit)

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.26, A.28, G.29, F.30, I.31, D.50, N.51, F.52, S.53, T.54, G.55, G.80, D.81, I.82, Q.101, A.102, A.103, G.105, T.120, A.143, A.144, S.145, Y.169, K.173, Y.196, N.198, V.199, Q.204 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.28, A:A.28, A:F.30, A:I.31, A:N.51, A:N.51, A:F.52, A:S.53, A:S.53, A:T.54, A:T.54, A:T.54, A:T.54, A:G.55, A:I.82, A:Q.101, A:A.103, A:T.120, A:Y.169, A:K.173, A:V.199, A:Q.204 pi-Stacking: A:Y.196 NAD.6: 26 residues within 4Å: Chain B: G.26, A.28, G.29, F.30, I.31, D.50, N.51, F.52, S.53, T.54, G.55, G.80, D.81, I.82, R.83, Q.101, A.102, A.103, T.120, A.143, A.144, Y.169, K.173, Y.196, N.198, V.199 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.196 Hydrogen bonds: B:G.26, B:A.28, B:F.30, B:I.31, B:N.51, B:N.51, B:F.52, B:S.53, B:S.53, B:T.54, B:T.54, B:T.54, B:T.54, B:G.55, B:I.82, B:Q.101, B:A.103, B:T.120, B:K.173, B:V.199 Water bridges: B:Q.204 pi-Stacking: B:Y.196

1 x GLY: GLYCINE(Non-covalent)

GLY.2: 6 residues within 4Å: Chain A: V.137, Q.138, S.139, G.188, K.190, K.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.190, A:K.260, A:K.260 Water bridges: A:F.140 Salt bridges: A:K.260

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

NA.3: 2 residues within 4Å: Chain A: Q.14, L.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.14 NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 1 residues within 4Å: Chain B: K.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.190, B:K.190

2 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)

UNL.5: 13 residues within 4Å: Chain A: N.198, A.212, V.213, K.216, W.217, Y.228, I.229, N.230, T.235, R.237, L.274, R.302, D.305 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.216 Hydrogen bonds: A:N.198, A:V.213, A:K.216, A:Y.228, A:N.230, A:N.230, A:R.302, A:R.302 Salt bridges: A:R.237, A:R.302 UNL.7: 13 residues within 4Å: Chain B: N.198, A.212, V.213, K.216, W.217, Y.228, I.229, N.230, T.235, R.237, L.274, R.302, D.305 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.198, B:V.213, B:K.216, B:Y.228, B:N.230, B:N.230, B:R.302, B:D.305 Salt bridges: B:R.237, B:R.302, B:R.302

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

SO4.8: 1 residues within 4Å: Chain B: R.271 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhatt, V.S. et al., Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase. TO BE PUBLISHED

Release Date

2011-05-25

Peptides

WbgU: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

WbgU

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