SMTL ID : 3mj4.1 (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, Y.82, P.84, H.85, I.86, H.88, T.241, D.242, Y.243, R.244, T.258, G.259, L.277, Y.334, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:L.277, A:Y.334 Hydrogen bonds: A:G.36, 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:R.244, A:T.258, A:R.364, A:Y.371, A:M.373 Water bridges: A:G.41, A:G.66, A:A.68, A:A.68, A:L.365, A:L.365, A:D.374 pi-Stacking: A:H.85, A:H.85 pi-Cation interactions: A:R.60 FAD.6: 31 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, P.260, L.277, Y.334, G.363, R.364, L.365, Y.371, N.372, M.373, V.376 31 PLIP interactions: 31 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.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.364, B:Y.371, B:M.373 Water bridges: B:A.37, B:G.41, B:H.63, B:A.68, B:A.68, B:R.198, B:T.258, B:L.365, B:D.374 pi-Stacking: B:H.85, B:H.85 pi-Cation interactions: B:R.60

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

UDP.2: 16 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, Y.370 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:F.175, A:T.180, A:T.180, A:Y.209, A:N.296, A:R.305, A:Y.370, A:Y.370 Water bridges: A:Q.183, A:R.198, A:Y.370 Salt bridges: A:R.198, A:R.198 pi-Stacking: A:Y.179 UDP.8: 13 residues within 4Å: Chain B: I.122, F.175, F.176, Y.179, T.180, W.184, V.195, T.196, R.198, V.199, Y.209, N.296, Y.370 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.175, B:T.180, B:T.180, B:Y.209, B:N.296, B:Y.370, B:Y.370 Salt bridges: B:R.198 pi-Stacking: B:Y.179

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.88, T.89, N.90, D.212, N.372, D.374, Q.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.90, A:N.90, A:N.372 GOL.4: 1 residues within 4Å: Chain A: F.140 No protein-ligand interaction detected (PLIP) GOL.5: 2 residues within 4Å: Chain A: L.137, F.145 No protein-ligand interaction detected (PLIP) GOL.9: 7 residues within 4Å: Chain B: H.88, T.89, N.90, D.212, N.372, D.374, Q.375 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.89, B:N.90, B:N.372, B:D.374 GOL.10: 1 residues within 4Å: Chain B: L.352 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain B: S.99, R.100, F.101, T.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.101 Water bridges: B:E.103 GOL.12: 3 residues within 4Å: Chain B: R.110, N.207, T.292 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.207

1 x XYL: Xylitol(Non-covalent)

XYL.7: 2 residues within 4Å: Chain B: R.105, P.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.105

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
A

B
I

UDP-galactopyranose mutase

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