SMTL ID : 3mj4.3 (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

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

FAD.1: 31 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, 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, G.363, R.364, Y.370, Y.371, N.372, M.373, V.376 30 PLIP interactions: 30 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:H.85, A:I.86, A:I.86, A:D.242, A:Y.243, A:R.244, A:R.364, A:Y.371, A:M.373 Water bridges: A:G.41, A:A.68, A:A.68, A:H.88, A:T.258, A:L.365, A:L.365 Salt bridges: A:R.364 pi-Cation interactions: A:H.85, A:H.85 FAD.5: 30 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, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, T.258, G.259, L.277, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 27 PLIP interactions: 27 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:T.258, B:R.364, B:Y.371, B:M.373 Water bridges: B:G.41, B:G.66, B:R.198, B:L.365, B:L.365, B:D.374 pi-Stacking: B:H.85, B:H.85

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

UDP.2: 15 residues within 4Å: Chain A: I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, T.196, R.198, V.199, Y.209, N.296, R.305, Y.335 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.175, A:T.180, A:T.180, A:T.180, A:Q.183, A:Y.209, A:N.296, A:Y.335 Salt bridges: A:R.198, A:R.305 pi-Stacking: A:Y.179 UDP.6: 16 residues within 4Å: Chain B: I.122, F.175, F.176, Y.179, T.180, Q.183, W.184, V.195, T.196, R.198, V.199, Y.209, N.296, R.305, Y.335, Y.370 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:F.175, B:T.180, B:T.180, B:Y.209, B:N.296, B:Y.335, B:Y.370, B:Y.370 Salt bridges: B:R.198, B:R.198, B:R.305 pi-Stacking: B:Y.179

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: H.88, N.90, D.212, N.372, D.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.90, A:N.372, A:D.374 GOL.4: 1 residues within 4Å: Chain A: F.140 No protein-ligand interaction detected (PLIP) GOL.7: 7 residues within 4Å: Chain B: H.88, T.89, N.90, S.91, D.212, N.372, D.374 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.89, B:T.89, B:N.90, B:N.90, B:S.91, B:N.372, B:D.374 GOL.9: 5 residues within 4Å: Chain B: R.47, R.100, L.381, F.384, R.385 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.47, B:R.100, B:R.385, B:R.385

1 x XYL: Xylitol(Non-covalent)

XYL.8: 3 residues within 4Å: Chain B: T.138, F.140, Q.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.138

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
C

B
F

UDP-galactopyranose mutase

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