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

E.coli's Putrescine receptor PotF complexed with Spermine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x SPM: SPERMINE(Non-covalent)

SPM.1: 15 residues within 4Å: Chain A: W.11, S.12, D.13, Y.14, N.39, S.59, S.61, E.159, I.204, W.218, D.221, Q.224, F.250, D.252, Y.288 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.11, A:D.13, A:F.250 Hydrogen bonds: A:S.12, A:D.13, A:S.59, A:S.61, A:S.61, A:D.252, A:Y.288

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

EDO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: D.13, I.15, H.285 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.13, A:H.285 EDO.4: 8 residues within 4Å: Chain A: S.61, F.62, R.65, K.323, V.324, Q.325, R.333 Ligands: EDO.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.65, A:K.323, A:Q.325, A:R.333, A:R.333 EDO.5: 3 residues within 4Å: Chain A: K.120, N.209, G.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.120 EDO.6: 4 residues within 4Å: Chain A: E.64, K.96, H.97, P.99 No protein-ligand interaction detected (PLIP) EDO.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.17: 11 residues within 4Å: Chain A: E.158, A.162, L.165, P.172, N.173, Y.180, L.322, K.323, Q.325, R.333 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.323, A:K.323, A:Q.325, A:R.333 EDO.18: 8 residues within 4Å: Chain A: D.87, L.90, W.109, N.290, N.292, K.293, T.296, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.87, A:D.87, A:W.109 EDO.19: 1 residues within 4Å: Chain A: K.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.147

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

PEG.7: 3 residues within 4Å: Chain A: G.126, E.127, N.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127

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

PGE.8: 3 residues within 4Å: Chain A: S.300, A.301, R.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.301, A:R.304, A:R.304

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

SO4.9: 4 residues within 4Å: Chain A: K.120, V.124, S.148, C.149 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.120 SO4.10: 4 residues within 4Å: Chain A: T.5, H.7, K.261, N.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.5, A:N.262 Salt bridges: A:H.7, A:K.261 SO4.11: 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

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

CL.12: 1 residues within 4Å: Chain A: E.82 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: D.13 Ligands: EDO.3 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: N.39 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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