SMTL ID : 1xel.1

UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 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.2: 2 residues within 4Å: Chain A: Q.334, Y.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.334 Water bridges: A:K.37, A:Q.194 NA.7: 1 residues within 4Å: Chain B: Q.91 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.91 Water bridges: B:Q.91, A:A.166 NA.8: 2 residues within 4Å: Chain B: Q.334, Y.336 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.336 Water bridges: B:K.37, B:Q.194

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, 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, S.124, Y.149, K.153, Y.177, F.178, P.180 Ligands: UPG.4, EDO.5 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.177 Hydrogen bonds: A:Y.11, A:I.12, A:N.32, A:N.32, A:L.33, A:C.34, A:N.35, A:N.35, A:D.58, A:I.59, A:F.80, A:G.82, A:K.84, A:S.122, A:Y.149, A:K.153 Water bridges: A:G.10, A:G.13, A:G.82, A:L.83, A:K.84, A:N.99, A:N.199 Salt bridges: A:K.84, A:K.84 NAD.9: 30 residues within 4Å: Chain B: G.7, S.9, G.10, Y.11, I.12, 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, S.124, Y.149, K.153, Y.177, F.178, P.180 Ligands: UPG.10, EDO.11 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.177 Hydrogen bonds: B:Y.11, B:I.12, B:N.32, B:N.32, B:L.33, B:C.34, B:N.35, B:N.35, B:D.58, B:I.59, B:F.80, B:G.82, B:K.84, B:S.122, B:K.153 Water bridges: B:G.10, B:G.13, B:G.82, B:L.83, B:K.84, B:N.99, B:N.199 Salt bridges: B:K.84, B:K.84

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.4: 22 residues within 4Å: Chain A: S.124, A.125, T.126, Y.149, Y.177, F.178, N.179, N.198, N.199, L.200, 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 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.218 Hydrogen bonds: A:S.124, A:N.179, A:N.199, A:L.200, A:A.216, A:F.218, A:Y.233, A:R.292, A:Y.299 Water bridges: A:T.126, A:N.179, A:M.201, A:R.231, A:R.231, A:D.232, A:R.292, A:R.292, A:D.295, A:D.295 Salt bridges: A:R.231, A:R.292, A:R.292 UPG.10: 22 residues within 4Å: Chain B: S.124, A.125, T.126, Y.149, Y.177, F.178, N.179, N.198, N.199, L.200, L.215, A.216, I.217, F.218, G.229, R.231, Y.233, V.269, R.292, D.295, Y.299 Ligands: NAD.9 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.218 Hydrogen bonds: B:S.124, B:Y.149, B:N.179, B:N.199, B:L.200, B:A.216, B:F.218, B:R.292, B:Y.299 Water bridges: B:T.126, B:N.179, B:M.201, B:R.231, B:R.231, B:R.231, B:D.232, B:R.292, B:R.292 Salt bridges: B:R.231, B:R.292, B:R.292

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: Y.11, N.35, G.190, E.191, D.192 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.35, A:G.190, A:D.192 Water bridges: A:N.35 EDO.11: 6 residues within 4Å: Chain B: Y.11, N.35, G.190, E.191, D.192 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.35, B:G.190, B:D.192 Water bridges: B:N.35

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: K.249, L.250, K.253, Y.259, E.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.253, A:Y.259 Water bridges: A:K.253 PEG.12: 5 residues within 4Å: Chain B: K.249, L.250, K.253, Y.259, E.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.253 Water bridges: B:K.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism. Biochemistry (1996)

Release Date

1997-02-12

Peptides

UDP-GALACTOSE 4-EPIMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-GALACTOSE 4-EPIMERASE

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