SMTL ID : 3frk.1

X-ray structure of QdtB from T. thermosaccharolyticum in complex with a PLP:TDP-3-aminoquinovose aldimine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x TQP: (2R,3R,4S,5S,6R)-3,5-dihydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

TQP.1: 30 residues within 4Å: Chain A: A.6, F.8, N.59, G.60, L.61, T.85, F.86, A.88, T.89, V.131, D.157, A.159, Q.160, S.181, Y.183, P.184, A.185, K.186, G.194, Y.283, L.307, H.309, Y.310 Chain B: N.30, W.31, F.32, I.33, Y.214, K.219, N.228 28 PLIP interactions: 16 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.86, A:A.88, A:V.131, A:A.159, A:Y.183, A:Y.183, A:P.184, B:W.31, B:I.33 Hydrogen bonds: A:G.60, A:L.61, A:Q.160, A:K.186, A:K.186, A:Y.283, A:Y.310, B:N.30, B:F.32, B:I.33, B:Y.214, B:Y.214, B:Y.214, B:N.228 Water bridges: A:Y.183 Salt bridges: A:H.309, B:K.219, B:K.219, B:K.219 TQP.2: 30 residues within 4Å: Chain A: N.30, W.31, F.32, I.33, Y.214, K.219, N.228 Chain B: F.5, A.6, F.8, N.59, G.60, L.61, T.85, F.86, A.88, T.89, V.131, D.157, A.159, Q.160, S.181, Y.183, A.185, K.186, G.194, Y.283, L.307, H.309, Y.310 33 PLIP interactions: 20 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.8, B:F.86, B:F.86, B:A.88, B:V.131, B:Y.183, B:Y.183, A:W.31, A:I.33, A:Y.214 Hydrogen bonds: B:N.59, B:G.60, B:L.61, B:Q.160, B:S.181, B:Y.183, B:K.186, B:K.186, B:Y.283, B:Y.310, B:Y.310, A:N.30, A:F.32, A:I.33, A:Y.214, A:Y.214, A:Y.214, A:N.228 Salt bridges: B:K.186, B:H.309, A:K.219, A:K.219, A:K.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose. Biochemistry (2009)

Release Date

2009-02-17

Peptides

QdtB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

QdtB