SMTL ID : 7oyy.1

E.coli's putrescine receptor variant PotF/D (4JDF) with mutation S247D in complex with spermidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 13 residues within 4Å: Chain A: W.11, T.12, E.13, Y.14, S.59, E.159, W.218, D.221, Q.224, W.250, D.252, Y.288 Ligands: EDO.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.11, A:Y.14, A:W.218, A:W.250 Hydrogen bonds: A:T.12, A:Y.288 Water bridges: A:S.59, A:S.59, A:S.59, A:E.159, A:D.252

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: D.87, L.90, W.109, A.289, N.290, A.291, N.292, K.293, T.296, Y.310, R.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.87, A:W.109 Water bridges: A:R.316

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

EDO.3: 9 residues within 4Å: Chain A: W.11, T.12, E.13, D.37, S.201, I.204, W.218, D.221 Ligands: SPD.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.221 EDO.4: 3 residues within 4Å: Chain A: T.296, R.304, E.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.304 Water bridges: A:T.296 EDO.5: 4 residues within 4Å: Chain A: D.326, P.327, K.328, R.331 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.326, A:K.328, A:R.331, A:R.331

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: Y.9, D.34, V.35, K.45, F.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.35, A:K.45 Water bridges: A:Y.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: S.59, A.60, Y.61, W.250, F.251 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroger, P. et al., Fine-tuning spermidine binding modes in the putrescine binding protein PotF. J.Biol.Chem. (2021)

Release Date

2021-12-01

Peptides

Putrescine-binding periplasmic protein PotF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putrescine-binding periplasmic protein PotF