SMTL ID : 1r66.1

Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: P.144, L.145 Chain B: P.144, L.145 Ligands: CL.4 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: P.144, L.145 Chain B: P.144, L.145 Ligands: CL.1 Ligand excluded by PLIP

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 29 residues within 4Å: Chain A: G.7, A.9, G.10, F.11, I.12, D.37, S.38, L.39, T.40, A.42, G.43, G.62, D.63, I.64, R.65, F.83, A.84, A.85, S.87, T.102, V.125, S.126, T.127, Y.151, K.155, C.178, C.179, N.180, N.181 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.12 Hydrogen bonds: A:A.9, A:F.11, A:I.12, A:G.13, A:S.38, A:S.38, A:L.39, A:T.40, A:T.40, A:I.64, A:F.83, A:A.85, A:S.87, A:T.102, A:T.102, A:K.155, A:N.181 Water bridges: A:G.10, A:Y.41, A:A.42, A:R.65, A:R.65, A:E.86, A:S.87, A:N.181, A:Q.186, A:Q.186, A:K.190 NAD.5: 29 residues within 4Å: Chain B: G.7, A.9, G.10, F.11, I.12, D.37, S.38, L.39, T.40, A.42, G.43, G.62, D.63, I.64, R.65, F.83, A.84, A.85, S.87, T.102, V.125, S.126, T.127, Y.151, K.155, C.178, C.179, N.180, N.181 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:I.12 Hydrogen bonds: B:A.9, B:F.11, B:I.12, B:G.13, B:S.38, B:S.38, B:L.39, B:T.40, B:T.40, B:I.64, B:F.83, B:A.85, B:S.87, B:T.102, B:T.102, B:K.155, B:N.181 Water bridges: B:G.10, B:Y.41, B:A.42, B:R.65, B:R.65, B:E.86, B:S.87, B:N.181, B:Q.186, B:Q.186, B:K.190

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.3: 18 residues within 4Å: Chain A: H.88, V.89, E.129, N.180, E.189, K.190, L.191, L.194, F.195, P.206, L.207, Y.208, N.213, R.215, N.250, R.274, H.277, Y.281 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.208 Hydrogen bonds: A:N.180, A:L.191, A:P.206, A:Y.208, A:R.215, A:N.250 Water bridges: A:H.88, A:K.190, A:R.215, A:R.274 Salt bridges: A:H.88, A:K.190, A:K.190, A:R.215, A:R.274, A:R.274 pi-Stacking: A:Y.208 TYD.6: 18 residues within 4Å: Chain B: H.88, V.89, E.129, N.180, E.189, K.190, L.191, L.194, F.195, P.206, L.207, Y.208, N.213, R.215, N.250, R.274, H.277, Y.281 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.208 Hydrogen bonds: B:N.180, B:L.191, B:P.206, B:Y.208, B:R.215, B:N.250 Water bridges: B:H.88, B:K.190, B:R.215, B:R.274 Salt bridges: B:H.88, B:K.190, B:K.190, B:R.215, B:R.274, B:R.274 pi-Stacking: B:Y.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allard, S.T.M. et al., High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae. J.Biol.Chem. (2004)

Release Date

2004-01-27

Peptides

TDP-glucose-4,6-dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

TDP-glucose-4,6-dehydratase