SMTL ID : 1i3k.1

MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: G.43, S.44, L.45 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: K.100, P.101, L.102 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: G.43, S.44, L.45 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: E.3, K.4, Y.80, S.81 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.310, S.312, E.316 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.312, H2O.4, H2O.11, H2O.11, H2O.13

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

NAD.3: 28 residues within 4Å: Chain A: G.9, A.11, G.12, Y.13, I.14, D.33, N.34, F.35, H.36, N.37, A.38, M.65, D.66, I.67, F.88, A.89, G.90, K.92, V.107, S.130, S.131, S.132, Y.157, K.161, Y.185, F.186, P.188 Ligands: UPG.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.185 Hydrogen bonds: A:G.9, A:Y.13, A:I.14, A:N.34, A:N.34, A:F.35, A:H.36, A:N.37, A:N.37, A:D.66, A:I.67, A:F.88, A:G.90, A:S.130, A:Y.157, A:K.161 Water bridges: A:G.12, A:G.15, A:G.90, A:L.91, A:K.92, A:K.92, A:P.188 Salt bridges: A:K.92, A:K.92 NAD.9: 27 residues within 4Å: Chain B: G.9, A.11, G.12, Y.13, I.14, D.33, N.34, F.35, H.36, N.37, A.38, M.65, D.66, I.67, F.88, A.89, G.90, K.92, V.107, S.130, S.131, S.132, Y.157, K.161, Y.185, P.188 Ligands: UPG.10 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.185 Hydrogen bonds: B:Y.13, B:I.14, B:N.34, B:N.34, B:F.35, B:H.36, B:N.37, B:N.37, B:D.66, B:I.67, B:F.88, B:G.90, B:S.130, B:Y.157, B:K.161 Water bridges: B:G.12, B:G.15, B:L.91, B:K.92, B:K.92, B:K.161 Salt bridges: B:K.92, B:K.92

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

UPG.4: 21 residues within 4Å: Chain A: S.132, A.133, T.134, Y.157, Y.185, F.186, N.187, N.206, N.207, L.208, L.223, N.224, V.225, F.226, G.237, R.239, Y.241, V.277, R.300, D.303 Ligands: NAD.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.208 Hydrogen bonds: A:S.132, A:N.187, A:N.206, A:L.208, A:N.224, A:F.226, A:R.300 Water bridges: A:N.187, A:M.209, A:G.237, A:R.239, A:R.300, A:R.300, A:D.303 Salt bridges: A:R.239, A:R.300, A:R.300 pi-Stacking: A:F.226 UPG.10: 20 residues within 4Å: Chain B: S.132, A.133, Y.157, F.186, N.187, N.206, N.207, L.208, L.223, N.224, V.225, F.226, G.237, R.239, Y.241, V.277, R.300, D.303, C.307 Ligands: NAD.9 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.208 Hydrogen bonds: B:N.187, B:N.206, B:L.208, B:N.224, B:F.226, B:Y.241 Water bridges: B:N.187, B:M.209, B:G.237, B:R.239, B:R.239, B:R.239, B:R.300, B:R.300 Salt bridges: B:R.239, B:R.300, B:R.300 pi-Stacking: B:F.226

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

EDO.5: 2 residues within 4Å: Chain A: A.25, G.26 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.25, A:G.26, A:G.26 EDO.11: 3 residues within 4Å: Chain B: A.121, H.122, G.123 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.121, B:H.122, B:H.122 EDO.12: 4 residues within 4Å: Chain B: G.71, Q.74, R.75, K.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Molecular basis for severe epimerase deficiency galactosemia. X-ray structure of the human V94m-substituted UDP-galactose 4-epimerase. J.Biol.Chem. (2001)

Release Date

2001-06-20

Peptides

UDP-GLUCOSE 4-EPIMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-GLUCOSE 4-EPIMERASE

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