SMTL ID : 6ot8.1

Bimetallic hexameric cage design 4 (BMC4) from cytochrome cb562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 21 residues within 4Å: Chain A: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:E.4, A:M.7, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 Salt bridges: A:H.8 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.7: 21 residues within 4Å: Chain B: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:E.4, B:M.7, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Salt bridges: B:H.8 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.13: 21 residues within 4Å: Chain C: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:E.4, C:M.7, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106 Salt bridges: C:H.8 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.19: 21 residues within 4Å: Chain D: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:E.4, D:M.7, D:P.45, D:F.61, D:F.65, D:F.65, D:F.65, D:L.68, D:R.106 Salt bridges: D:H.8 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.25: 21 residues within 4Å: Chain E: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:E.4, E:M.7, E:P.45, E:F.61, E:F.65, E:F.65, E:F.65, E:L.68, E:R.106 Salt bridges: E:H.8 pi-Cation interactions: E:R.106 Metal complexes: E:H.102 HEC.31: 21 residues within 4Å: Chain F: L.3, E.4, M.7, H.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:E.4, F:M.7, F:P.45, F:F.61, F:F.65, F:F.65, F:F.65, F:L.68, F:R.106 Salt bridges: F:H.8 pi-Cation interactions: F:R.106 Metal complexes: F:H.102

18 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.5, H.8 Chain F: E.5, H.8 Ligands: ZN.32 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Metal complexes: A:E.5, A:E.5, A:H.8, F:E.5, F:H.8 ZN.3: 4 residues within 4Å: Chain A: D.21, N.22, E.25 Chain C: H.77 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.21, A:E.25, A:E.25, C:H.77, H2O.3 ZN.4: 4 residues within 4Å: Chain A: D.12, H.16 Chain F: A.1, E.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.16 ZN.8: 5 residues within 4Å: Chain B: E.5, H.8 Chain E: E.5, H.8 Ligands: ZN.26 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Metal complexes: B:E.5, B:E.5, B:H.8, E:E.5, E:H.8 ZN.9: 4 residues within 4Å: Chain A: H.77 Chain B: D.21, N.22, E.25 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.21, B:E.25, B:E.25, A:H.77, H2O.8 ZN.10: 4 residues within 4Å: Chain B: D.12, H.16 Chain E: A.1, E.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.16 ZN.14: 5 residues within 4Å: Chain C: E.5, H.8 Chain D: E.5, H.8 Ligands: ZN.20 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Metal complexes: C:E.5, C:E.5, C:H.8, D:E.5, D:H.8 ZN.15: 4 residues within 4Å: Chain B: H.77 Chain C: D.21, N.22, E.25 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.77, C:D.21, C:E.25, C:E.25, H2O.13 ZN.16: 4 residues within 4Å: Chain C: D.12, H.16 Chain D: A.1, E.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.16 ZN.20: 5 residues within 4Å: Chain C: E.5, H.8 Chain D: E.5, H.8 Ligands: ZN.14 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:E.5, C:H.8, D:E.5, D:E.5, D:H.8 ZN.21: 4 residues within 4Å: Chain D: D.21, N.22, E.25 Chain F: H.77 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: D:D.21, D:E.25, D:E.25, F:H.77, H2O.17 ZN.22: 4 residues within 4Å: Chain C: A.1, E.2 Chain D: D.12, H.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.16 ZN.26: 5 residues within 4Å: Chain B: E.5, H.8 Chain E: E.5, H.8 Ligands: ZN.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E Metal complexes: B:E.5, B:H.8, E:E.5, E:E.5, E:H.8 ZN.27: 4 residues within 4Å: Chain D: H.77 Chain E: D.21, N.22, E.25 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:D.21, E:E.25, E:E.25, D:H.77, H2O.22 ZN.28: 4 residues within 4Å: Chain B: A.1, E.2 Chain E: D.12, H.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.16 ZN.32: 5 residues within 4Å: Chain A: E.5, H.8 Chain F: E.5, H.8 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Metal complexes: F:E.5, F:E.5, F:H.8, A:E.5, A:H.8 ZN.33: 4 residues within 4Å: Chain E: H.77 Chain F: D.21, N.22, E.25 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.21, F:E.25, F:E.25, E:H.77, H2O.27 ZN.34: 4 residues within 4Å: Chain A: A.1, E.2 Chain F: D.12, H.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.16

6 x FE: FE (III) ION(Non-functional Binders)

FE.5: 5 residues within 4Å: Ligands: HAE.6, FE.11, HAE.12, FE.17, HAE.18 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.6, HAE.12 FE.11: 5 residues within 4Å: Ligands: FE.5, HAE.6, HAE.12, FE.17, HAE.18 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.6, HAE.12 FE.17: 5 residues within 4Å: Ligands: FE.5, HAE.6, FE.11, HAE.12, HAE.18 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: HAE.18 FE.23: 5 residues within 4Å: Ligands: HAE.24, FE.29, HAE.30, FE.35, HAE.36 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.24, HAE.30 FE.29: 5 residues within 4Å: Ligands: FE.23, HAE.24, HAE.30, FE.35, HAE.36 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.24, HAE.30 FE.35: 5 residues within 4Å: Ligands: FE.23, HAE.24, FE.29, HAE.30, HAE.36 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: HAE.36

6 x HAE: ACETOHYDROXAMIC ACID(Covalent)

HAE.6: 12 residues within 4Å: Chain A: A.23, K.27, A.79, K.80, C.82 Chain B: A.24, K.27 Ligands: FE.5, FE.11, HAE.12, FE.17, HAE.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.23 Hydrogen bonds: A:K.27 Water bridges: A:K.80 HAE.12: 12 residues within 4Å: Chain B: A.23, K.27, A.79, K.80, C.82 Chain C: A.24, K.27 Ligands: FE.5, HAE.6, FE.11, FE.17, HAE.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.23 Hydrogen bonds: B:K.27 Water bridges: B:K.80 HAE.18: 12 residues within 4Å: Chain A: A.24, K.27 Chain C: A.23, K.27, A.79, K.80, C.82 Ligands: FE.5, HAE.6, FE.11, HAE.12, FE.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.23 Hydrogen bonds: C:K.27 Water bridges: C:K.80 HAE.24: 12 residues within 4Å: Chain D: A.23, K.27, A.79, K.80, C.82 Chain E: A.24, K.27 Ligands: FE.23, FE.29, HAE.30, FE.35, HAE.36 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.23 Hydrogen bonds: D:K.27 Water bridges: D:K.80 HAE.30: 12 residues within 4Å: Chain E: A.23, K.27, A.79, K.80, C.82 Chain F: A.24, K.27 Ligands: FE.23, HAE.24, FE.29, FE.35, HAE.36 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.23 Hydrogen bonds: E:K.27 Water bridges: E:K.80 HAE.36: 12 residues within 4Å: Chain D: A.24, K.27 Chain F: A.23, K.27, A.79, K.80, C.82 Ligands: FE.23, HAE.24, FE.29, HAE.30, FE.35 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.23 Hydrogen bonds: F:K.27 Water bridges: F:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golub, E. et al., Constructing protein polyhedra via orthogonal chemical interactions. Nature (2020)

Release Date

2020-01-29

Peptides

Soluble cytochrome b562: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Soluble cytochrome b562