SMTL ID : 4rpk.2 (1 other biounit)

Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with tetrafluorinated substrate analog UDP-F4-Galf

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: V.13, G.14, G.16, F.17, F.18, L.37, E.38, R.39, R.40, G.45, N.46, Y.62, G.63, A.64, H.65, L.66, T.223, D.224, W.225, F.226, T.244, G.245, P.246, R.249, L.263, Y.327, Y.328, G.359, R.360, L.361, L.367, D.368, M.369, H.370, A.372 Ligands: 3UA.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:L.263, A:Y.327 Hydrogen bonds: A:G.16, A:F.17, A:F.18, A:R.39, A:R.39, A:R.40, A:N.46, A:N.46, A:H.65, A:L.66, A:L.66, A:D.224, A:W.225, A:R.249, A:R.360, A:L.367, A:D.368, A:M.369, A:H.370 Water bridges: A:G.19, A:G.45, A:N.46, A:A.47, A:H.68, A:R.180, A:R.180, A:T.244 pi-Stacking: A:H.65, A:H.65 pi-Cation interactions: A:R.39 FAD.3: 35 residues within 4Å: Chain B: V.13, G.14, G.16, F.17, F.18, L.37, E.38, R.39, R.40, G.45, N.46, Y.62, G.63, A.64, H.65, L.66, T.223, D.224, W.225, F.226, T.244, G.245, P.246, L.263, R.292, Y.327, Y.328, G.359, R.360, L.367, D.368, M.369, H.370, A.372 Ligands: 3UA.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.263, B:Y.327 Hydrogen bonds: B:F.17, B:F.18, B:R.39, B:R.40, B:N.46, B:N.46, B:H.65, B:L.66, B:L.66, B:D.224, B:W.225, B:T.244, B:R.360, B:L.367, B:M.369, B:H.370 Water bridges: B:G.16, B:G.16, B:H.68, B:R.180 pi-Stacking: B:H.65, B:H.65

2 x 3UA: (2R,5S)-5-[(1R)-1,2-dihydroxyethyl]-3,3,4,4-tetrafluorotetrahydrofuran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

3UA.2: 25 residues within 4Å: Chain A: A.64, L.66, H.89, V.91, F.102, L.141, F.157, V.158, Y.161, T.162, Q.165, W.166, N.177, I.178, R.180, L.181, Y.191, F.192, V.280, N.282, N.284, R.292, Y.328, Y.366 Ligands: FAD.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.181 Hydrogen bonds: A:F.157, A:Y.161, A:T.162, A:W.166, A:N.282, A:N.282, A:N.284, A:R.292, A:Y.328, A:Y.328, A:Y.366 Water bridges: A:Q.165, A:Q.165, A:R.180, A:R.180, A:R.360 Salt bridges: A:R.180, A:R.180, A:R.292, A:R.292 pi-Stacking: A:Y.161 Halogen bonds: A:A.64 3UA.4: 25 residues within 4Å: Chain B: A.64, L.66, H.89, V.91, F.102, L.141, F.157, V.158, Y.161, T.162, Q.165, W.166, N.177, I.178, R.180, L.181, Y.191, F.192, V.280, N.282, N.284, R.292, Y.328, Y.366 Ligands: FAD.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.181 Hydrogen bonds: B:F.157, B:Y.161, B:W.166, B:Y.191, B:N.282, B:N.284, B:R.292, B:Y.328 Water bridges: B:Y.161, B:Y.161, B:Q.165, B:R.180, B:R.180, B:R.360, B:Y.366 Salt bridges: B:R.180, B:R.180, B:R.292, B:R.292 pi-Stacking: B:Y.161 Halogen bonds: B:A.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Straaten, K.E. et al., Structural Basis of Ligand Binding to UDP-Galactopyranose Mutase from Mycobacterium tuberculosis Using Substrate and Tetrafluorinated Substrate Analogues. J.Am.Chem.Soc. (2015)

Release Date

2015-01-21

Peptides

UDP-galactopyranose mutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

UDP-galactopyranose mutase

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