SMTL ID : 6ye7.1 (1 other biounit)

E.coli's Putrescine receptor PotF complexed with Cadaverine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)

N2P.1: 12 residues within 4Å: Chain A: W.11, S.12, D.13, Y.14, N.39, S.59, W.218, D.221, Q.224, F.250, D.252, Y.288 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.14, A:W.218, A:W.218, A:F.250 Hydrogen bonds: A:S.12, A:S.59, A:S.59, A:Y.288 Water bridges: A:S.12, A:D.13

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

EDO.2: 6 residues within 4Å: Chain A: S.12, D.13, Y.14, I.15, Y.33, V.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.13, A:D.13 EDO.3: 5 residues within 4Å: Chain A: T.175, K.176, A.177, D.178, K.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.177, A:D.178, A:D.178 EDO.4: 6 residues within 4Å: Chain A: L.46, M.47, A.48, G.49, V.71 Ligands: PGE.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.46 EDO.5: 3 residues within 4Å: Chain A: S.300, A.301, E.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.301, A:E.302 EDO.7: 1 residues within 4Å: Chain A: K.96 No protein-ligand interaction detected (PLIP) EDO.8: 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 EDO.10: 6 residues within 4Å: Chain A: L.67, T.68, G.70, F.72, P.74, F.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.72 Water bridges: A:G.70 EDO.11: 5 residues within 4Å: Chain A: T.5, L.6, H.7, K.261, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.262 Water bridges: A:T.5 EDO.12: 6 residues within 4Å: Chain A: E.40, D.155, P.157, T.334, W.337, K.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.155, A:W.337, A:K.341 EDO.13: 4 residues within 4Å: Chain A: P.311, P.312, A.313, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.313, A:R.316, A:R.316 Water bridges: A:D.314 EDO.15: 5 residues within 4Å: Chain A: K.147, P.193, N.194, I.195, R.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.147, A:R.196 Water bridges: A:K.147, A:R.196 EDO.17: 3 residues within 4Å: Chain A: T.181, R.335, K.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.335, A:R.335, A:K.339

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 5 residues within 4Å: Chain A: A.21, E.24, K.25 Ligands: PEG.9, CL.19 No protein-ligand interaction detected (PLIP)

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

PEG.9: 7 residues within 4Å: Chain A: Q.3, E.24, K.25, G.28, I.29, K.30 Ligands: PG4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.3

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

PGE.14: 8 residues within 4Å: Chain A: G.49, S.50, A.69, G.70, V.71, A.258, D.259 Ligands: EDO.4 No protein-ligand interaction detected (PLIP)

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.16: 9 residues within 4Å: Chain A: L.90, L.93, W.109, A.249, F.251, R.316, A.317, L.319, T.321 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.90, A:F.251, A:R.316 Water bridges: A:R.316, A:T.321

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

CL.18: 2 residues within 4Å: Chain A: Q.202, N.205 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: E.24, K.30, V.31 Ligands: PG4.6 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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