SMTL ID : 6z3c.1

High resolution structure of RgNanOx

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.18, T.19, G.20, Y.21, F.22, L.42, D.43, P.44, E.45, N.46, A.77, T.78, P.79, N.80, L.82, H.83, E.100, K.101, V.129, W.170, K.171, H.183, H.186, K.308, P.309, L.317 Ligands: FLC.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.21, A:F.22, A:F.22 Hydrogen bonds: A:T.19, A:Y.21, A:F.22, A:E.45, A:N.46, A:N.80, A:N.80, A:H.83, A:E.100, A:K.101 Water bridges: A:G.20, A:G.23 Salt bridges: A:K.171, A:K.171 NAD.3: 28 residues within 4Å: Chain B: G.18, T.19, G.20, Y.21, F.22, L.42, D.43, P.44, E.45, N.46, A.77, T.78, P.79, N.80, L.82, H.83, E.100, K.101, P.102, V.129, W.170, K.171, H.183, H.186, K.308, P.309, L.317 Ligands: FLC.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.21, B:F.22, B:F.22 Hydrogen bonds: B:T.19, B:Y.21, B:F.22, B:E.45, B:N.46, B:N.80, B:N.80, B:H.83, B:H.183 Water bridges: B:G.20, B:G.23 Salt bridges: B:K.171, B:K.171

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 11 residues within 4Å: Chain A: Y.21, K.101, R.158, K.171, H.183, H.184, H.186, M.305, Y.306, G.307 Ligands: NAD.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.306 Hydrogen bonds: A:H.183, A:G.307 Water bridges: A:R.158, A:R.158, A:R.158 Salt bridges: A:K.101, A:R.158, A:K.171, A:H.183, A:H.183, A:H.184, A:H.184, A:H.186 FLC.4: 11 residues within 4Å: Chain B: Y.21, K.101, R.158, K.171, H.183, H.184, H.186, M.305, Y.306, G.307 Ligands: NAD.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.306 Hydrogen bonds: B:H.183, B:M.305, B:G.307 Water bridges: B:R.158, B:R.158, B:R.158, B:R.158, B:H.186, B:H.186, B:M.305 Salt bridges: B:K.101, B:R.158, B:K.171, B:H.183, B:H.183, B:H.184, B:H.184, B:H.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bell, A. et al., Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J.Biol.Chem. (2020)

Release Date

2020-06-03

Peptides

Gfo/Idh/MocA family oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Gfo/Idh/MocA family oxidoreductase