- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- hetero-2-4-2-2-mer
- Ligands
- 2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
ZN.2: 4 residues within 4Å:- Chain B: C.192, C.195, C.290, C.292
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.192, B:C.195, B:C.290, B:C.292
ZN.5: 4 residues within 4Å:- Chain C: C.192, C.195, C.290, C.292
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:C.192, C:C.195, C:C.290, C:C.292
ZN.16: 4 residues within 4Å:- Chain G: C.192, C.195, C.290, C.292
4 PLIP interactions:4 interactions with chain G- Metal complexes: G:C.192, G:C.195, G:C.290, G:C.292
ZN.19: 4 residues within 4Å:- Chain H: C.192, C.195, C.290, C.292
4 PLIP interactions:4 interactions with chain H- Metal complexes: H:C.192, H:C.195, H:C.290, H:C.292
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 8 residues within 4Å:- Chain B: C.195, R.199, S.202, R.210, E.212, V.284, I.285, W.287
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.202, B:R.210, B:R.210, B:E.212, B:I.285
GOL.18: 8 residues within 4Å:- Chain G: C.195, R.199, S.202, R.210, E.212, V.284, I.285, W.287
6 PLIP interactions:6 interactions with chain G- Hydrogen bonds: G:S.202, G:R.210, G:R.210, G:E.212, G:E.212, G:I.285
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.6: 4 residues within 4Å:- Chain C: S.58, E.59, Y.60, T.91
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Y.60, C:T.91
- pi-Stacking: C:Y.60, C:Y.60
ATP.20: 4 residues within 4Å:- Chain H: S.58, E.59, Y.60, T.91
4 PLIP interactions:4 interactions with chain H- Hydrogen bonds: H:Y.60, H:T.91
- pi-Stacking: H:Y.60, H:Y.60
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 6 residues within 4Å:- Chain C: L.174, S.177, R.179, S.271
- Chain E: N.7, M.9
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:S.177, C:R.179, C:R.179, C:S.271
EDO.8: 7 residues within 4Å:- Chain C: F.18, E.19, R.51
- Chain E: G.155, S.350, L.351, W.353
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain E- Hydrogen bonds: C:E.19, E:L.351, E:W.353
EDO.21: 6 residues within 4Å:- Chain H: L.174, S.177, R.179, S.271
- Chain J: N.7, M.9
4 PLIP interactions:4 interactions with chain H- Hydrogen bonds: H:S.177, H:R.179, H:R.179, H:S.271
EDO.22: 7 residues within 4Å:- Chain H: F.18, E.19, R.51
- Chain J: G.155, S.350, L.351, W.353
2 PLIP interactions:2 interactions with chain J- Hydrogen bonds: J:L.351, J:W.353
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.9: 17 residues within 4Å:- Chain E: A.43, Q.52, G.53, G.56, E.57, E.60, S.152, F.153, H.154, E.167, K.257, E.261
- Chain G: L.222
- Ligands: PO4.10, MG.11, MG.12, MG.13
15 PLIP interactions:1 interactions with chain G, 14 interactions with chain E- Hydrogen bonds: G:L.222, E:E.60, E:S.152, E:F.153
- Water bridges: E:H.154, E:G.155, E:R.171, E:K.257, E:K.257, E:K.257, E:Q.264, E:Q.264
- Salt bridges: E:K.257, E:K.257
- pi-Stacking: E:H.154
ADP.23: 17 residues within 4Å:- Chain B: L.222
- Chain J: A.43, Q.52, G.53, G.56, E.57, E.60, S.152, F.153, H.154, E.167, K.257, E.261
- Ligands: PO4.24, MG.25, MG.26, MG.27
16 PLIP interactions:15 interactions with chain J, 1 interactions with chain B- Hydrogen bonds: J:E.57, J:E.60, J:E.60, J:S.152, J:F.153, B:L.222
- Water bridges: J:G.155, J:R.171, J:K.257, J:K.257, J:K.257, J:Q.264, J:Q.264
- Salt bridges: J:K.257, J:K.257
- pi-Stacking: J:H.154
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.10: 9 residues within 4Å:- Chain E: E.57, R.61, E.167, R.171, E.261
- Ligands: ADP.9, MG.11, MG.12, MG.13
15 PLIP interactions:15 interactions with chain E- Hydrogen bonds: E:E.167
- Water bridges: E:E.57, E:E.57, E:R.61, E:R.61, E:R.61, E:R.171, E:R.171, E:R.171, E:R.171, E:R.171, E:K.257, E:K.257
- Salt bridges: E:R.61, E:R.171
PO4.24: 9 residues within 4Å:- Chain J: E.57, R.61, E.167, R.171, E.261
- Ligands: ADP.23, MG.25, MG.26, MG.27
15 PLIP interactions:15 interactions with chain J- Hydrogen bonds: J:E.167
- Water bridges: J:E.57, J:E.57, J:E.57, J:E.57, J:R.61, J:R.171, J:R.171, J:R.171, J:R.171, J:R.171, J:K.257, J:K.257
- Salt bridges: J:R.61, J:R.171
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.11: 7 residues within 4Å:- Chain E: E.170, R.171, L.245, K.257, E.261
- Ligands: ADP.9, PO4.10
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:E.261, H2O.7, H2O.7, H2O.7
MG.12: 6 residues within 4Å:- Chain E: E.60, R.61, C.151, E.167
- Ligands: ADP.9, PO4.10
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:E.167, H2O.7, H2O.7, H2O.8
MG.13: 3 residues within 4Å:- Chain E: E.57
- Ligands: ADP.9, PO4.10
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:E.57, H2O.7, H2O.7, H2O.7
MG.25: 7 residues within 4Å:- Chain J: E.170, R.171, L.245, K.257, E.261
- Ligands: ADP.23, PO4.24
4 PLIP interactions:1 interactions with chain J, 3 Ligand-Water interactions- Metal complexes: J:E.261, H2O.16, H2O.16, H2O.16
MG.26: 6 residues within 4Å:- Chain J: E.60, R.61, C.151, E.167
- Ligands: ADP.23, PO4.24
4 PLIP interactions:1 interactions with chain J, 3 Ligand-Water interactions- Metal complexes: J:E.167, H2O.16, H2O.16, H2O.16
MG.27: 3 residues within 4Å:- Chain J: E.57
- Ligands: ADP.23, PO4.24
4 PLIP interactions:1 interactions with chain J, 3 Ligand-Water interactions- Metal complexes: J:E.57, H2O.16, H2O.16, H2O.16
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ghilarov, D. et al., Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol. Cell (2019)
- Release Date
- 2019-01-30
- Peptides
- Bacteriocin microcin B17: AF
Microcin B17-processing protein McbB: BCGH
Microcin B17-processing protein McbC: DI
Microcin B17-processing protein McbD: EJ - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AF
AB
1C
2G
1H
2D
CI
CE
DJ
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- hetero-2-4-2-2-mer
- Ligands
- 2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ghilarov, D. et al., Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol. Cell (2019)
- Release Date
- 2019-01-30
- Peptides
- Bacteriocin microcin B17: AF
Microcin B17-processing protein McbB: BCGH
Microcin B17-processing protein McbC: DI
Microcin B17-processing protein McbD: EJ - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AF
AB
1C
2G
1H
2D
CI
CE
DJ
D