SMTL ID : 3mj4.4 (4 other biounits)

Crystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

1 x URM: (((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride(Non-covalent)

URM.1: 19 residues within 4Å: Chain A: P.84, I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, T.196, R.198, V.199, Y.209, F.210, N.296, R.305, Y.370, N.372 Ligands: FAD.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:F.175, A:T.180, A:T.180, A:T.180, A:Q.183, A:R.198, A:N.296, A:R.305, A:Y.370, A:N.372 Water bridges: A:R.198 Salt bridges: A:R.198 pi-Stacking: A:Y.179

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 32 residues within 4Å: Chain A: V.35, G.36, G.38, F.39, A.40, V.58, D.59, R.60, R.61, G.66, N.67, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, T.258, G.259, P.260, L.277, Y.334, G.363, R.364, Y.370, Y.371, N.372, M.373, V.376 Ligands: URM.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.277, A:Y.334, A:Y.370 Hydrogen bonds: A:G.38, A:F.39, A:A.40, A:R.60, A:R.60, A:R.61, A:R.61, A:N.67, A:N.67, A:H.85, A:I.86, A:I.86, A:D.242, A:Y.243, A:T.258, A:R.364, A:Y.371, A:M.373 Water bridges: A:A.68, A:A.68, A:D.374 Salt bridges: A:R.364 pi-Stacking: A:H.85, A:H.85 pi-Cation interactions: A:R.60 FAD.5: 34 residues within 4Å: Chain B: V.35, G.36, G.38, F.39, A.40, V.58, D.59, R.60, R.61, G.66, N.67, Y.82, G.83, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, P.260, L.277, Y.334, Y.335, G.363, R.364, L.365, Y.371, N.372, M.373, V.376 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.277, B:Y.334 Hydrogen bonds: B:G.38, B:F.39, B:A.40, B:R.60, B:R.61, B:R.61, B:N.67, B:N.67, B:H.85, B:I.86, B:I.86, B:D.242, B:Y.243, B:R.244, B:R.364, B:Y.371, B:M.373 Water bridges: B:D.374 pi-Stacking: B:H.85, B:H.85

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.88, T.89, N.90, D.212, N.372, D.374 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.88, A:T.89, A:N.90, A:N.90, A:D.212, A:N.372 GOL.4: 1 residues within 4Å: Chain A: F.140 No protein-ligand interaction detected (PLIP) GOL.7: 1 residues within 4Å: Chain B: F.140 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain B: E.103, R.224, N.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.103, B:E.103, B:R.224, B:N.228

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.6: 15 residues within 4Å: Chain B: I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, R.198, V.199, Y.209, N.296, R.305, Y.335, Y.370 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:F.175, B:T.180, B:T.180, B:T.180, B:Y.209, B:N.296, B:Y.370, B:Y.370 Salt bridges: B:R.198, B:R.305 pi-Stacking: B:Y.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Partha, S.K. et al., Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase. J.Mol.Biol. (2010)

Release Date

2010-10-20

Peptides

UDP-galactopyranose mutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
J

UDP-galactopyranose mutase

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