SMTL ID : 3sxp.1

Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-pentamer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.17, A.19, G.20, F.21, V.22, D.43, K.44, S.58, L.59, G.60, A.75, D.76, I.77, N.78, Q.97, A.98, A.99, A.136, S.137, S.138, Y.161, K.165, Y.186, V.189, K.197 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.186 Hydrogen bonds: A:A.19, A:A.19, A:F.21, A:V.22, A:K.44, A:G.60, A:D.76, A:D.76, A:I.77, A:Q.97, A:A.99, A:K.165, A:V.189 Water bridges: A:G.20, A:G.23, A:L.59, A:L.59 Salt bridges: A:K.197, A:K.197 pi-Stacking: A:Y.186 NAD.2: 25 residues within 4Å: Chain B: G.17, A.19, G.20, F.21, V.22, D.43, K.44, S.58, L.59, G.60, A.75, D.76, I.77, N.78, Q.97, A.98, A.99, A.136, S.137, S.138, Y.161, K.165, Y.186, V.189, K.197 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.186 Hydrogen bonds: B:A.19, B:A.19, B:F.21, B:V.22, B:K.44, B:G.60, B:D.76, B:I.77, B:Q.97, B:A.99, B:K.165, B:V.189, B:V.189 Water bridges: B:G.20, B:G.20, B:T.114, B:T.114 Salt bridges: B:K.197, B:K.197 NAD.3: 26 residues within 4Å: Chain C: G.17, A.19, G.20, F.21, V.22, L.42, D.43, K.44, S.58, L.59, G.60, A.75, D.76, I.77, Q.97, A.98, A.99, A.136, S.137, S.138, Y.161, K.165, Y.186, N.188, V.189, K.197 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.186 Hydrogen bonds: C:A.19, C:A.19, C:F.21, C:V.22, C:K.44, C:G.60, C:D.76, C:D.76, C:I.77, C:Q.97, C:A.99, C:Y.161, C:K.165, C:V.189 Salt bridges: C:K.197, C:K.197 NAD.4: 25 residues within 4Å: Chain D: G.17, A.19, G.20, F.21, V.22, D.43, K.44, S.58, L.59, G.60, A.75, D.76, I.77, Q.97, A.98, A.99, A.136, S.137, S.138, Y.161, K.165, Y.186, N.188, V.189, K.197 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:Y.186 Hydrogen bonds: D:A.19, D:A.19, D:F.21, D:V.22, D:K.44, D:G.60, D:D.76, D:I.77, D:Q.97, D:A.99, D:K.165, D:V.189, D:V.189 Water bridges: D:A.19, D:G.20, D:G.20, D:L.59, D:L.59, D:K.197, D:K.197 Salt bridges: D:K.197, D:K.197 pi-Stacking: D:Y.186 NAD.5: 25 residues within 4Å: Chain E: G.17, A.19, G.20, F.21, V.22, L.42, D.43, K.44, S.58, L.59, G.60, A.75, D.76, I.77, Q.97, A.98, A.99, A.136, S.137, S.138, Y.161, K.165, Y.186, V.189, K.197 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:Y.186 Hydrogen bonds: E:A.19, E:A.19, E:F.21, E:V.22, E:K.44, E:G.60, E:D.76, E:D.76, E:I.77, E:Q.97, E:A.99, E:Y.161, E:K.165, E:V.189, E:K.197 Water bridges: E:A.19, E:L.59 Salt bridges: E:K.197, E:K.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaik, M.M. et al., The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori. Biochim.Biophys.Acta (2011)

Release Date

2012-02-08

Peptides

ADP-L-glycero-D-mannoheptose-6-epimerase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

ADP-L-glycero-D-mannoheptose-6-epimerase