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

E.coli's Putrescine receptor PotF in its closed apo state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: M.47 No protein-ligand interaction detected (PLIP) EDO.2: 1 residues within 4Å: Chain A: H.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.199 EDO.4: 5 residues within 4Å: Chain A: E.64, L.67, K.96, H.97, P.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 EDO.7: 2 residues within 4Å: Chain A: A.21, E.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.24 EDO.8: 2 residues within 4Å: Chain A: Y.116, N.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.116, A:N.237 EDO.10: 3 residues within 4Å: Chain A: S.12, D.37, S.201 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.12, A:S.12, A:S.201 Water bridges: A:D.37, A:D.37 EDO.11: 4 residues within 4Å: Chain A: S.12, D.13, Y.33, V.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.13 Water bridges: A:Y.14 EDO.13: 5 residues within 4Å: Chain A: W.223, F.240, S.241, I.242, G.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.242 EDO.14: 5 residues within 4Å: Chain A: D.37, S.38, D.155, H.199, S.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.38, A:H.199, A:S.200, A:S.201 Water bridges: A:S.200 EDO.15: 6 residues within 4Å: Chain A: D.87, L.90, W.109, N.290, T.296, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.87, A:W.109 Water bridges: A:T.296

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

PEG.3: 4 residues within 4Å: Chain A: L.46, M.47, G.49, S.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.47 PEG.5: 6 residues within 4Å: Chain A: L.90, L.93, W.109, F.251, R.316, L.319 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: T.68, G.70, F.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.68, A:F.72 PEG.9: 3 residues within 4Å: Chain A: G.126, E.127, N.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.127, A:N.128 PEG.12: 3 residues within 4Å: Chain A: H.281, D.284, H.285 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.281, A:D.284, A:D.284

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

SO4.16: 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

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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