SMTL ID : 6yed.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 4 residues within 4Å: Chain A: G.220, D.221, Q.224 Ligands: CL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.220 Water bridges: A:S.59, A:Q.224

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

PEG.2: 3 residues within 4Å: Chain A: P.88, E.89, K.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.92 PEG.3: 9 residues within 4Å: Chain A: K.96, N.166, D.171, P.172, N.173, K.318, L.319, F.320, K.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.166, A:N.173, A:K.323

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

EDO.4: 7 residues within 4Å: Chain A: W.109, A.110, T.111, I.242, Y.288, A.289, I.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.289 EDO.5: 3 residues within 4Å: Chain A: H.7, V.32, D.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.34 Water bridges: A:H.7 EDO.6: 2 residues within 4Å: Chain A: P.17, A.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.17 Water bridges: A:A.21 EDO.7: 6 residues within 4Å: Chain A: S.59, A.60, S.61, H.97, F.250, F.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.61, A:F.251, A:F.251 EDO.8: 6 residues within 4Å: Chain A: K.84, N.85, L.86, P.88, K.293, A.294 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: E.89, K.293, A.313, R.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.89 EDO.10: 3 residues within 4Å: Chain A: D.155, P.157, E.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.155, A:E.158 EDO.11: 4 residues within 4Å: Chain A: K.244, P.307, P.312, V.315 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.307 EDO.12: 4 residues within 4Å: Chain A: R.192, R.196, Y.197, F.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.192, A:R.196, A:F.198, A:F.198 EDO.13: 6 residues within 4Å: Chain A: P.88, L.91, K.92, A.95, N.101 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain A: A.95, P.99, D.100 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.100

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

CL.15: 3 residues within 4Å: Chain A: W.11, D.252 Ligands: PGE.1 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: E.159, W.218, F.250 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
A

Putrescine-binding periplasmic protein

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