SMTL ID : 7oyv.1 (1 other biounit)

E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88A S247D in complex with spermidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 3IZ: (2~{R})-1-[(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-yl]oxypropan-2-amine(Non-covalent)

3IZ.1: 7 residues within 4Å: Chain A: Q.3, A.21, E.24, K.25, G.28, I.29, K.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.25, A:K.30 Water bridges: A:K.30

2 x JFN: (2R)-1-methoxypropan-2-amine(Non-covalent)

JFN.2: 3 residues within 4Å: Chain A: P.312, A.313, R.316 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.312 Hydrogen bonds: A:R.316 JFN.3: 2 residues within 4Å: Chain A: Q.3, K.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.3, A:Q.3, A:K.4

1 x SPD: SPERMIDINE(Non-covalent)

SPD.4: 13 residues within 4Å: Chain A: W.11, T.12, D.13, Y.14, N.39, S.59, Y.61, E.159, W.218, D.221, W.250, D.252, Y.288 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.11, A:W.11, A:W.218 Hydrogen bonds: A:T.12, A:S.59, A:S.59, A:D.252, A:Y.288 Water bridges: A:T.12, A:N.39

2 x 3IE: (2~{S})-1-methoxypropan-2-amine(Non-covalent)

3IE.5: 4 residues within 4Å: Chain A: L.90, L.93, W.109, R.316 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.93 3IE.6: 5 residues within 4Å: Chain A: Q.3, K.4, T.5, K.261, N.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.5, A:K.261, A:N.262 Water bridges: A:H.7

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

CL.7: 4 residues within 4Å: Chain A: 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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putrescine-binding periplasmic protein

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