SMTL ID : 3mj4.5 (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: 30 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, L.277, E.325, Y.334, G.363, R.364, Y.371, N.372, M.373, V.376 27 PLIP interactions: 27 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.61, 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.66, A:A.68, A:A.68, A:D.374 pi-Stacking: A:H.85, A:H.85 pi-Cation interactions: A:R.60 FAD.7: 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, Y.335, G.363, R.364, Y.371, N.372, M.373, V.376 29 PLIP interactions: 29 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: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:A.37, B:G.66, B:L.365, B:L.365, B:D.374 Salt bridges: B:R.364 pi-Stacking: B:H.85, B:H.85 pi-Cation interactions: B:R.60

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

UDP.2: 12 residues within 4Å: Chain A: I.122, F.175, F.176, Y.179, T.180, W.184, V.195, R.198, V.199, Y.209, N.296, Y.370 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.175, A:T.180, A:Y.209, A:Y.209, A:N.296, A:Y.370, A:Y.370 Salt bridges: A:R.198 pi-Stacking: A:Y.179 UDP.8: 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:T.180, B:Q.183, B:Y.209, B:N.296, B:Y.370 Water bridges: B:Y.335 Salt bridges: B:R.198, B:R.305 pi-Stacking: B:Y.179

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.89, N.90, D.212, D.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.90, A:N.90, A:D.374 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.6: 4 residues within 4Å: Chain A: S.99, R.100, T.102, N.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.99, A:N.228 Water bridges: A:E.103, A:E.103 GOL.9: 6 residues within 4Å: Chain B: H.88, N.90, D.212, N.372, D.374, Q.375 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.90, B:N.90, B:N.372, B:D.374 GOL.10: 5 residues within 4Å: Chain B: S.99, R.100, F.101, T.102, N.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.99, B:N.228 Water bridges: B:E.103, B:E.103 GOL.11: 3 residues within 4Å: Chain B: F.145, S.148, V.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.148

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
E

B
G

UDP-galactopyranose mutase

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