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

E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y S247D in complex with spermidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

1 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 15 residues within 4Å: Chain A: W.11, T.12, D.13, Y.14, N.39, S.59, D.156, E.159, I.204, W.218, D.221, Q.224, W.250, D.252, Y.288 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.11, A:W.11, A:W.218, A:W.218, A:W.250 Hydrogen bonds: A:N.39, A:S.59, A:S.59, A:D.221, A:Y.288 Water bridges: A:S.59, A:D.156, A:E.159, A:E.159, A:Q.322

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

3IE.2: 6 residues within 4Å: Chain A: Q.3, K.4, T.5, H.7, K.261, N.262 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.261 Hydrogen bonds: A:T.5, A:N.262 3IE.3: 6 residues within 4Å: Chain A: L.46, M.47, A.48, G.49, A.69, V.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.49, A:G.49

1 x 4SW: (2~{S})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine(Non-covalent)

4SW.4: 8 residues within 4Å: Chain A: L.90, L.93, W.109, F.251, A.289, N.290, Y.310, R.316 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.90, A:W.109, A:F.251 Water bridges: A:R.316

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

CL.5: 5 residues within 4Å: Chain A: S.59, A.60, S.61, W.250, F.251 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: S.300, A.301 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

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