SMTL ID : 6ye6.2 (1 other biounit)

E.coli's Putrescine receptor PotF complexed with Agmatine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

2 x ONT: (2~{S})-1-(2-methoxyethoxy)propan-2-amine(Non-covalent)

ONT.1: 11 residues within 4Å: Chain A: E.89, L.90, L.93, W.109, A.249, F.251, R.316, A.317, L.319, F.320, T.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.316 ONT.3: 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:E.24 Hydrogen bonds: A:E.24 Water bridges: A:G.28

1 x AG2: AGMATINE(Non-covalent)

AG2.2: 14 residues within 4Å: Chain A: W.11, S.12, D.13, Y.14, N.39, S.59, E.159, W.218, D.221, Q.224, M.248, F.250, D.252, Y.288 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.11, A:W.11, A:W.218 Hydrogen bonds: A:S.12, A:N.39, A:S.59, A:Y.288 Water bridges: A:S.12, A:E.159, A:E.159 Salt bridges: A:E.159, A:D.252 pi-Cation interactions: A:F.250

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

JFN.4: 1 residues within 4Å: Chain A: P.297 No protein-ligand interaction detected (PLIP) JFN.5: 5 residues within 4Å: Chain A: S.12, V.35, F.36, D.37, S.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.37 Water bridges: A:D.37, A:S.201 JFN.6: 4 residues within 4Å: Chain A: K.122, G.126, E.127, N.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127 JFN.7: 6 residues within 4Å: Chain A: L.46, M.47, G.49, S.50, V.71, D.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.49 Water bridges: A:D.259 JFN.8: 5 residues within 4Å: Chain A: I.15, A.16, P.17, V.20, Y.33 No protein-ligand interaction detected (PLIP) JFN.9: 6 residues within 4Å: Chain A: L.67, T.68, A.69, G.70, F.72, F.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.67 JFN.10: 6 residues within 4Å: Chain A: T.175, K.176, A.177, D.178, K.328, I.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.175, A:A.177, A:D.178, A:K.328 JFN.11: 5 residues within 4Å: Chain A: V.299, S.300, A.301, E.302, R.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.301, A:R.304

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 2 residues within 4Å: Chain A: R.335, K.339 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.335, A:K.339 SO4.13: 3 residues within 4Å: Chain A: K.147, G.150, R.196 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.147, A:V.151, A:R.196 Salt bridges: A:K.147, A:R.196 SO4.14: 2 residues within 4Å: Chain A: H.281, H.285 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.281, A:H.285

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

CL.15: 3 residues within 4Å: Chain A: P.327, K.328, R.331 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroger, P. et al., A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF. Structure (2021)

Release Date

2021-01-20

Peptides

Putrescine-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Putrescine-binding periplasmic protein

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