SMTL ID : 2o7p.1

The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: K.157, T.166, A.167, M.168, A.169, W.175, S.198, S.199, A.200, T.201, A.204, D.205, I.237, D.238, S.239, Q.240, R.242, H.283, L.284, L.286, A.305, G.306, P.307, T.308, L.309, A.312 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.201 Hydrogen bonds: A:K.157, A:K.157, A:A.169, A:S.198, A:S.199, A:S.199, A:T.201, A:D.205, A:S.239, A:R.242, A:G.306, A:T.308, A:T.308, A:L.309 pi-Stacking: A:W.175, A:H.283 NAP.2: 21 residues within 4Å: Chain B: K.157, W.175, S.198, S.199, A.200, T.201, D.205, I.237, D.238, S.239, R.242, H.283, L.284, L.286, E.304, A.305, G.306, P.307, T.308, L.309, A.312 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.175 Hydrogen bonds: B:K.157, B:S.198, B:S.199, B:I.237, B:S.239, B:S.239, B:R.242, B:E.304, B:E.304, B:G.306, B:G.306, B:T.308, B:T.308, B:T.308, B:L.309 Salt bridges: B:R.242 pi-Stacking: B:W.175, B:H.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stenmark, P. et al., The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism. J.Mol.Biol. (2007)

Release Date

2007-02-13

Peptides

Riboflavin biosynthesis protein ribD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Riboflavin biosynthesis protein ribD