SMTL ID : 1nzc.2 (1 other biounit)

The high resolution structures of RmlC from Streptococcus suis in complex with dTDP-D-xylose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: E.52 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, H2O.7, H2O.9

2 x TDX: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE(Non-covalent)

TDX.2: 15 residues within 4Å: Chain A: Q.61, N.63, R.73, H.76, E.78, K.82, N.127, Y.140, W.146, K.151, D.180 Chain B: H.29, R.33, F.36, E.38 25 PLIP interactions: 9 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:F.36, A:W.146 Hydrogen bonds: B:H.29, B:E.38, B:E.38, A:Q.61, A:E.78, A:K.82, A:N.127, A:Y.140 Water bridges: B:R.33, B:R.33, A:R.73, A:R.73, A:K.151, A:K.151 Salt bridges: B:R.33, B:R.33, A:R.73, A:H.76, A:H.76, A:K.151 pi-Stacking: B:F.36, A:W.146, A:W.146 TDX.3: 14 residues within 4Å: Chain A: H.29, R.33, F.36, E.38 Chain B: Q.61, N.63, R.73, H.76, E.78, K.82, N.127, Y.140, W.146, D.180 23 PLIP interactions: 7 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:F.36, B:W.146 Hydrogen bonds: A:E.38, B:Q.61, B:E.78, B:K.82, B:N.127, B:Y.140 Water bridges: A:R.33, A:R.33, B:E.78, B:E.78, B:W.146, B:K.151, B:S.177 Salt bridges: A:R.33, A:R.33, B:R.73, B:H.76, B:H.76 pi-Stacking: A:F.36, B:W.146, B:W.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., High-Resolution Structures of RmlC from Streptococcus suis in Complex with Substrate Analogs Locate the Active Site of This Class of Enzyme. Structure (2003)

Release Date

2003-06-24

Peptides

dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

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