SMTL ID : 1lrj.1

Crystal Structure of E. coli UDP-Galactose 4-Epimerase Complexed with UDP-N-Acetylglucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: K.37, Q.334, Y.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:Q.334 NA.2: 1 residues within 4Å: Chain A: Q.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.91, A:Q.91 NA.6: 3 residues within 4Å: Chain B: K.37, Q.334, Y.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.334 Water bridges: B:Q.334 NA.7: 1 residues within 4Å: Chain B: Q.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.91, B:Q.91

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

NAD.3: 30 residues within 4Å: Chain A: G.7, S.9, G.10, Y.11, I.12, L.30, D.31, N.32, L.33, C.34, N.35, S.36, G.57, D.58, I.59, R.60, F.80, A.81, G.82, K.84, N.99, S.122, S.123, Y.149, K.153, Y.177, F.178, P.180, N.199 Ligands: UD1.4 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.177, A:P.180 Hydrogen bonds: A:G.7, A:Y.11, A:I.12, A:G.13, A:N.32, A:N.32, A:L.33, A:C.34, A:N.35, A:N.35, A:S.36, A:S.36, A:I.59, A:R.60, A:F.80, A:G.82, A:N.99, A:Y.149, A:K.153, A:N.199 Water bridges: A:G.10, A:N.35, A:L.83, A:K.84, A:K.153 Salt bridges: A:K.84, A:K.84 NAD.8: 30 residues within 4Å: Chain B: G.7, S.9, G.10, Y.11, I.12, L.30, D.31, N.32, L.33, C.34, N.35, S.36, G.57, D.58, I.59, R.60, F.80, A.81, G.82, K.84, N.99, S.122, S.123, Y.149, K.153, Y.177, F.178, P.180, N.199 Ligands: UD1.9 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:Y.177, B:P.180 Hydrogen bonds: B:G.7, B:Y.11, B:I.12, B:G.13, B:N.32, B:N.32, B:L.33, B:C.34, B:N.35, B:N.35, B:S.36, B:S.36, B:I.59, B:R.60, B:F.80, B:G.82, B:N.99, B:K.153, B:Y.177, B:N.199 Water bridges: B:G.10, B:N.35, B:L.83, B:K.84, B:K.153 Salt bridges: B:K.84, B:K.84

2 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.4: 25 residues within 4Å: Chain A: K.84, V.86, S.124, A.125, T.126, Y.149, Y.177, F.178, N.179, N.198, N.199, L.200, Y.203, L.215, A.216, I.217, F.218, G.229, R.231, Y.233, V.269, R.292, D.295, Y.299 Ligands: NAD.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.200 Hydrogen bonds: A:V.86, A:A.125, A:Y.177, A:N.179, A:L.200, A:A.216, A:F.218, A:R.292, A:Y.299 Water bridges: A:N.198, A:N.199, A:R.231 Salt bridges: A:R.231, A:R.292 UD1.9: 25 residues within 4Å: Chain B: K.84, V.86, S.124, A.125, T.126, Y.149, Y.177, F.178, N.179, N.198, N.199, L.200, Y.203, L.215, A.216, I.217, F.218, G.229, R.231, Y.233, V.269, R.292, D.295, Y.299 Ligands: NAD.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.200 Hydrogen bonds: B:V.86, B:A.125, B:T.126, B:Y.149, B:Y.177, B:N.179, B:L.200, B:A.216, B:F.218, B:R.292, B:Y.299 Water bridges: B:N.198, B:N.199, B:R.231 Salt bridges: B:R.231, B:R.292

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 5 residues within 4Å: Chain A: K.249, L.250, K.253, Y.259, E.309 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.309, A:E.309 PGE.10: 5 residues within 4Å: Chain B: K.249, L.250, K.253, Y.259, E.309 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.309, B:E.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Structural analysis of the Y299C mutant of Escherichia coli UDP-galactose 4-epimerase. Teaching an old dog new tricks. J.Biol.Chem. (2002)

Release Date

2002-07-26

Peptides

UDP-glucose 4-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-glucose 4-epimerase

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