SMTL ID : 8asz.1

PotF with mutations S87Y and A182D in complex with Agmatine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

1 x AG2: AGMATINE(Non-covalent)

AG2.1: 11 residues within 4Å: Chain A: W.11, S.12, D.13, Y.14, S.59, W.218, D.221, Q.224, F.250, D.252, Y.288 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.11 Hydrogen bonds: A:D.13 Water bridges: A:W.11, A:N.39, A:P.58, A:S.59, A:S.59, A:E.159, A:E.159, A:E.159, A:Q.224, A:D.252 Salt bridges: A:D.252 pi-Cation interactions: A:W.218

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

EDO.2: 6 residues within 4Å: Chain A: I.15, P.17, V.20, A.21, Y.33 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.31, A:Y.33 EDO.7: 5 residues within 4Å: Chain A: K.261, N.262, K.263, D.264, E.265 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.262, A:D.264 EDO.8: 1 residues within 4Å: Chain A: P.297 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.297 EDO.9: 5 residues within 4Å: Chain A: E.305, P.307, Y.310, P.311, P.312 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: K.230 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: S.133, D.135, Y.167, K.244, E.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.133, A:S.133, A:K.244 EDO.12: 9 residues within 4Å: Chain A: W.223, S.226, N.227, K.230, F.287, E.302, V.303, N.306, I.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.302, A:N.306 Water bridges: A:S.226, A:K.230, A:K.230 EDO.13: 8 residues within 4Å: Chain A: W.11, S.12, D.13, Y.14, I.15, Y.33, V.35 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.13, A:D.13 Water bridges: A:Y.14, A:I.15 EDO.14: 5 residues within 4Å: Chain A: K.230, K.233, N.234, G.235 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.233 Water bridges: A:G.235 EDO.15: 6 residues within 4Å: Chain A: V.131, D.132, S.241, I.242, P.243, K.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.132 Water bridges: A:I.242

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: N.39, S.59, Y.61, D.156, E.158, E.159, M.248, L.322 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.159, A:E.159 Water bridges: A:N.39, A:N.39, A:N.39, A:S.59, A:S.59, A:D.156, A:D.156 GOL.4: 12 residues within 4Å: Chain A: D.87, L.90, W.109, A.289, N.290, A.291, N.292, K.293, T.296, Y.310, P.311, R.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.109, A:N.290 Water bridges: A:R.316

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

PEG.5: 9 residues within 4Å: Chain A: K.147, S.148, G.150, V.151, R.192, P.193, N.194, I.195, R.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.147, A:R.192, A:P.193, A:R.196, A:R.196 Water bridges: A:G.150, A:R.196 PEG.6: 6 residues within 4Å: Chain A: T.181, T.185, V.332, R.335, A.336, K.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.185, A:R.335, A:K.339

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain A: S.59, A.60, Y.61, F.250, F.251 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroeger, P. et al., A fluorescent biosensor for the visualization of Agmatine. To Be Published

Release Date

2024-03-06

Peptides

Putrescine-binding periplasmic protein PotF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putrescine-binding periplasmic protein PotF