SMTL ID : 2po3.1

Crystal Structure Analysis of DesI in the presence of its TDP-sugar product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x T4K: (2R,3R,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]-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)

T4K.1: 33 residues within 4Å: Chain A: L.22, V.23, G.24, R.25, P.26, N.75, A.76, T.77, T.99, F.100, A.102, T.103, D.171, A.173, H.174, S.195, H.197, A.198, T.199, K.200, G.207, Y.298, R.327, Y.329, F.330 Chain B: Q.45, W.46, L.47, S.48, N.49, F.227, F.229, N.241 30 PLIP interactions: 23 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.100, A:F.100, A:A.102, A:A.173, A:T.199, A:F.330, B:N.49 Hydrogen bonds: A:A.76, A:T.77, A:T.77, A:T.77, A:H.174, A:S.195, A:S.195, A:K.200, B:Q.45, B:L.47, B:S.48, B:N.49, B:N.241 Water bridges: A:H.197, A:T.199, A:R.327, A:R.327, A:Y.329, A:Y.329, B:N.226 Salt bridges: A:K.200, A:R.327, A:R.327 T4K.2: 30 residues within 4Å: Chain A: Q.45, W.46, L.47, S.48, N.49, F.227, F.229, N.241 Chain B: L.22, V.23, G.24, R.25, P.26, N.75, A.76, T.77, T.99, F.100, A.102, D.171, A.173, H.174, S.195, H.197, T.199, K.200, G.207, R.327, Y.329, F.330 27 PLIP interactions: 19 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.100, B:F.100, B:A.102, B:A.173, B:T.199, B:Y.329, B:F.330, A:N.49 Hydrogen bonds: B:A.76, B:T.77, B:T.77, B:H.174, B:S.195, B:S.195, B:T.199, B:K.200, B:R.327, B:Y.329, A:Q.45, A:L.47, A:S.48, A:N.49, A:N.241 Water bridges: B:H.197, B:E.206, A:N.226, A:N.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Molecular Architecture of DesI: A Key Enzyme in the Biosynthesis of Desosamine. Biochemistry (2007)

Release Date

2007-08-14

Peptides

4-dehydrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-dehydrase