SMTL ID : 1kew.1

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

TYD.1: 18 residues within 4Å: Chain A: H.85, V.86, D.87, E.135, N.196, E.205, K.206, L.207, L.210, P.222, I.223, Y.224, R.231, N.266, R.297, H.300, Y.304, Y.357 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.224 Hydrogen bonds: A:N.196, A:N.196, A:L.207, A:P.222, A:Y.224, A:R.231, A:N.266 Water bridges: A:H.85, A:R.231, A:Y.304 Salt bridges: A:H.85, A:R.231, A:R.297, A:R.297 pi-Stacking: A:Y.224 TYD.6: 18 residues within 4Å: Chain B: H.85, V.86, D.87, E.135, N.196, E.205, K.206, L.207, L.210, P.222, I.223, Y.224, R.231, N.266, R.297, H.300, Y.304, Y.357 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.224 Hydrogen bonds: B:N.196, B:N.196, B:L.207, B:P.222, B:Y.224, B:R.231, B:N.266, B:Y.357 Water bridges: B:H.85, B:K.206, B:R.231, B:R.297 Salt bridges: B:H.85, B:R.231, B:R.297, B:R.297 pi-Stacking: B:Y.224

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.32, K.33, L.34, T.35, A.37, G.38, A.57, D.58, I.59, L.80, A.81, A.82, S.84, T.99, I.131, S.132, T.133, Y.167, K.171, C.194, S.195, N.196, N.197, K.206 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.12 Hydrogen bonds: A:A.9, A:A.9, A:F.11, A:I.12, A:K.33, A:L.34, A:T.35, A:T.35, A:I.59, A:L.80, A:A.82, A:S.84, A:T.99, A:T.99, A:Y.167, A:K.171, A:N.197, A:K.206, A:K.206 Water bridges: A:G.10, A:G.13, A:Y.36, A:A.37, A:S.84, A:S.84 Salt bridges: A:K.206 pi-Cation interactions: A:H.239 NAD.7: 29 residues within 4Å: Chain B: G.7, A.9, G.10, F.11, I.12, D.32, K.33, L.34, T.35, A.37, G.38, A.57, D.58, I.59, L.80, A.81, A.82, S.84, T.99, I.131, S.132, T.133, Y.167, K.171, C.194, S.195, N.196, N.197, K.206 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.12 Hydrogen bonds: B:A.9, B:A.9, B:F.11, B:I.12, B:G.13, B:K.33, B:L.34, B:T.35, B:T.35, B:D.58, B:I.59, B:L.80, B:A.82, B:S.84, B:T.99, B:K.171, B:N.197, B:K.206, B:K.206 Water bridges: B:G.10, B:A.37, B:S.84, B:S.84 pi-Cation interactions: B:H.239

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: D.296 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.296, A:D.296 GOL.4: 7 residues within 4Å: Chain A: E.157, T.158, R.179, G.253, E.254, T.255, K.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.157, A:T.255, A:T.255, A:K.310 GOL.5: 5 residues within 4Å: Chain A: N.262, K.264, T.322, F.323, E.324 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.262, A:K.264, A:F.323, A:E.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allard, S.T. et al., Toward a structural understanding of the dehydratase mechanism. Structure (2002)

Release Date

2002-01-25

Peptides

dTDP-D-glucose 4,6-dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dTDP-D-glucose 4,6-dehydratase

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