SMTL ID : 4iil.1

Crystal Structure of RfuA (TP0298) of T. pallidum Bound to Riboflavin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.1: 23 residues within 4Å: Chain A: G.41, S.46, P.47, V.48, Y.49, Q.81, W.84, N.104, P.105, A.106, D.127, Q.143, Q.146, Q.177, Y.179, I.186, W.211, I.235, G.237, G.238, F.257, D.258, M.275 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:P.105, A:A.106, A:Y.179, A:W.211 Hydrogen bonds: A:S.46, A:S.46, A:D.127, A:Q.143, A:Y.179, A:G.237, A:D.258, A:D.258 Water bridges: A:V.48, A:D.127 pi-Stacking: A:W.211, A:W.211, A:W.211

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: S.158, N.166, D.168, K.169, K.170, D.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.166, A:D.230 Water bridges: A:N.166 NA.3: 6 residues within 4Å: Chain A: S.158, A.159, S.160, A.165, N.166, A.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.158

1 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: P.180, T.183, Q.184 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.183, H2O.5, H2O.8

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: N.260, V.274, E.276, R.309, I.311 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.276, A:R.309, A:R.309 Water bridges: A:N.260 EDO.6: 3 residues within 4Å: Chain A: K.304, G.339, T.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deka, R.K. et al., Evidence for an ABC-type riboflavin transporter system in pathogenic spirochetes. MBio (2013)

Release Date

2013-02-27

Peptides

Membrane lipoprotein TpN38(b): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane lipoprotein TpN38(b)