- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- monomer
- Ligands
- 1 x SPD: SPERMIDINE(Non-covalent)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 8 residues within 4Å:- Chain A: W.11, T.12, D.13, Y.14, I.15, Y.33, V.35
- Ligands: EDO.11
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.13, A:Y.14
EDO.3: 7 residues within 4Å:- Chain A: Y.9, V.35, F.36, D.37, S.38, V.41
- Ligands: EDO.15
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.37, A:D.37, A:D.37, A:S.38
EDO.4: 9 residues within 4Å:- Chain A: L.90, L.93, W.109, A.249, F.251, R.316, L.319
- Ligands: EDO.5, EDO.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.316
- Water bridges: A:L.319
EDO.5: 6 residues within 4Å:- Chain A: E.89, L.93, R.316, A.317
- Ligands: EDO.4, EDO.10
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.316
- Water bridges: A:R.316, A:R.316, A:R.316
EDO.6: 4 residues within 4Å:- Chain A: E.144, K.147, P.193, N.194
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.144, A:K.147
- Water bridges: A:E.144
EDO.7: 4 residues within 4Å:- Chain A: N.166, Y.167, G.169, E.245
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.167, A:G.169
EDO.9: 5 residues within 4Å:- Chain A: K.120, N.209, G.210, N.234, V.236
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.120
EDO.10: 8 residues within 4Å:- Chain A: D.87, E.89, L.90, W.109, R.316
- Ligands: EDO.4, EDO.5, GOL.19
2 PLIP interactions:2 interactions with chain A- Water bridges: A:E.89, A:R.316
EDO.11: 6 residues within 4Å:- Chain A: I.15, P.17, V.20, A.21, Y.33
- Ligands: EDO.2
2 PLIP interactions:2 interactions with chain A- Water bridges: A:V.31, A:Y.33
EDO.12: 5 residues within 4Å:- Chain A: E.64, K.96, H.97, K.323, V.324
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.64, A:H.97, A:V.324
EDO.13: 3 residues within 4Å:- Chain A: P.88, E.89, K.92
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.89
EDO.15: 7 residues within 4Å:- Chain A: H.7, Y.9, D.34, K.45, F.53
- Ligands: EDO.3, EDO.16
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.34, A:K.45
- Water bridges: A:Y.9, A:Y.9
EDO.16: 2 residues within 4Å:- Chain A: K.45
- Ligands: EDO.15
No protein-ligand interaction detected (PLIP)EDO.17: 5 residues within 4Å:- Chain A: N.22, K.25, E.26, R.275
- Ligands: GOL.20
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.26
EDO.18: 8 residues within 4Å:- Chain A: W.223, S.226, N.227, K.230, F.287, E.302, N.306, I.309
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.226, A:N.227, A:K.230
- Water bridges: A:E.302
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.19: 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, R.316
- Ligands: EDO.10
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:W.109, A:T.296, A:T.296
- Water bridges: A:R.316
GOL.20: 7 residues within 4Å:- Chain A: D.18, N.22, R.275, D.277, V.278, H.281
- Ligands: EDO.17
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.22, A:R.275, A:D.277
- Water bridges: A:D.18, A:Y.272
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kroger, P. et al., Fine-tuning spermidine binding modes in the putrescine binding protein PotF. J.Biol.Chem. (2021)
- Release Date
- 2021-12-01
- Peptides
- Putrescine-binding periplasmic protein: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- monomer
- Ligands
- 1 x SPD: SPERMIDINE(Non-covalent)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kroger, P. et al., Fine-tuning spermidine binding modes in the putrescine binding protein PotF. J.Biol.Chem. (2021)
- Release Date
- 2021-12-01
- Peptides
- Putrescine-binding periplasmic protein: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A