SMTL ID : 6ovh.1

Cryo-EM structure of Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x HEC: HEME C(Covalent)

HEC.1: 13 residues within 4Å: Chain A: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:P.45, A:F.61, A:F.65, A:R.106 Salt bridges: A:H.8 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.8: 13 residues within 4Å: Chain B: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:P.45, B:F.61, B:F.65, B:R.106 Salt bridges: B:H.8 pi-Stacking: B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.15: 13 residues within 4Å: Chain C: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:P.45, C:F.61, C:F.65, C:R.106 Salt bridges: C:H.8 pi-Stacking: C:H.102 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.20: 13 residues within 4Å: Chain D: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:P.45, D:F.61, D:F.65, D:R.106 Salt bridges: D:H.8 pi-Stacking: D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.27: 13 residues within 4Å: Chain E: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:L.3, E:M.7, E:P.45, E:F.61, E:F.65, E:R.106 Salt bridges: E:H.8 pi-Stacking: E:H.102 pi-Cation interactions: E:R.106 Metal complexes: E:H.102 HEC.34: 13 residues within 4Å: Chain F: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:L.3, F:M.7, F:P.45, F:F.61, F:F.65, F:R.106 Salt bridges: F:H.8 pi-Stacking: F:H.102 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEC.38: 13 residues within 4Å: Chain G: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain G, Hydrophobic interactions: G:L.3, G:M.7, G:P.45, G:F.61, G:F.65, G:R.106 Salt bridges: G:H.8 pi-Stacking: G:H.102 pi-Cation interactions: G:R.106 Metal complexes: G:H.102 HEC.43: 13 residues within 4Å: Chain H: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain H, Hydrophobic interactions: H:L.3, H:M.7, H:P.45, H:F.61, H:F.65, H:R.106 Salt bridges: H:H.8 pi-Stacking: H:H.102 pi-Cation interactions: H:R.106 Metal complexes: H:H.102 HEC.48: 13 residues within 4Å: Chain I: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain I, Hydrophobic interactions: I:L.3, I:M.7, I:P.45, I:F.61, I:F.65, I:R.106 Salt bridges: I:H.8 pi-Stacking: I:H.102 pi-Cation interactions: I:R.106 Metal complexes: I:H.102 HEC.55: 13 residues within 4Å: Chain J: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain J, Hydrophobic interactions: J:L.3, J:M.7, J:P.45, J:F.61, J:F.65, J:R.106 Salt bridges: J:H.8 pi-Stacking: J:H.102 pi-Cation interactions: J:R.106 Metal complexes: J:H.102 HEC.60: 13 residues within 4Å: Chain K: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain K, Hydrophobic interactions: K:L.3, K:M.7, K:P.45, K:F.61, K:F.65, K:R.106 Salt bridges: K:H.8 pi-Stacking: K:H.102 pi-Cation interactions: K:R.106 Metal complexes: K:H.102 HEC.65: 13 residues within 4Å: Chain L: L.3, E.4, M.7, H.8, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain L, Hydrophobic interactions: L:L.3, L:M.7, L:P.45, L:F.61, L:F.65, L:R.106 Salt bridges: L:H.8 pi-Stacking: L:H.102 pi-Cation interactions: L:R.106 Metal complexes: L:H.102

24 x HAE: ACETOHYDROXAMIC ACID(Covalent)

HAE.2: 4 residues within 4Å: Chain A: C.63 Ligands: FE.14, HAE.16, HAE.21 Ligand excluded by PLIP HAE.3: 6 residues within 4Å: Chain A: A.23, C.82 Chain F: C.82 Ligands: FE.7, HAE.36, HAE.40 Ligand excluded by PLIP HAE.9: 4 residues within 4Å: Chain B: C.63 Ligands: FE.11, HAE.35, HAE.56 Ligand excluded by PLIP HAE.10: 6 residues within 4Å: Chain B: A.23, C.82 Chain C: C.82 Ligands: FE.12, HAE.17, HAE.50 Ligand excluded by PLIP HAE.16: 4 residues within 4Å: Chain C: C.63 Ligands: HAE.2, FE.14, HAE.21 Ligand excluded by PLIP HAE.17: 6 residues within 4Å: Chain C: A.23, C.82 Chain I: C.82 Ligands: HAE.10, FE.12, HAE.50 Ligand excluded by PLIP HAE.21: 4 residues within 4Å: Chain D: C.63 Ligands: HAE.2, FE.14, HAE.16 Ligand excluded by PLIP HAE.22: 6 residues within 4Å: Chain D: A.23, C.82 Chain H: C.82 Ligands: FE.23, HAE.45, HAE.67 Ligand excluded by PLIP HAE.28: 4 residues within 4Å: Chain E: C.63 Ligands: HAE.39, FE.42, HAE.44 Ligand excluded by PLIP HAE.29: 6 residues within 4Å: Chain E: A.23, C.82 Chain J: C.82 Ligands: FE.33, HAE.57, HAE.62 Ligand excluded by PLIP HAE.35: 4 residues within 4Å: Chain F: C.63 Ligands: HAE.9, FE.11, HAE.56 Ligand excluded by PLIP HAE.36: 6 residues within 4Å: Chain F: A.23, C.82 Chain G: C.82 Ligands: HAE.3, FE.7, HAE.40 Ligand excluded by PLIP HAE.39: 4 residues within 4Å: Chain G: C.63 Ligands: HAE.28, FE.42, HAE.44 Ligand excluded by PLIP HAE.40: 6 residues within 4Å: Chain A: C.82 Chain G: A.23, C.82 Ligands: HAE.3, FE.7, HAE.36 Ligand excluded by PLIP HAE.44: 4 residues within 4Å: Chain H: C.63 Ligands: HAE.28, HAE.39, FE.42 Ligand excluded by PLIP HAE.45: 6 residues within 4Å: Chain H: A.23, C.82 Chain L: C.82 Ligands: HAE.22, FE.23, HAE.67 Ligand excluded by PLIP HAE.49: 4 residues within 4Å: Chain I: C.63 Ligands: FE.51, HAE.61, HAE.66 Ligand excluded by PLIP HAE.50: 6 residues within 4Å: Chain B: C.82 Chain I: A.23, C.82 Ligands: HAE.10, FE.12, HAE.17 Ligand excluded by PLIP HAE.56: 4 residues within 4Å: Chain J: C.63 Ligands: HAE.9, FE.11, HAE.35 Ligand excluded by PLIP HAE.57: 6 residues within 4Å: Chain J: A.23, C.82 Chain K: C.82 Ligands: HAE.29, FE.33, HAE.62 Ligand excluded by PLIP HAE.61: 4 residues within 4Å: Chain K: C.63 Ligands: HAE.49, FE.51, HAE.66 Ligand excluded by PLIP HAE.62: 6 residues within 4Å: Chain E: C.82 Chain K: A.23, C.82 Ligands: HAE.29, FE.33, HAE.57 Ligand excluded by PLIP HAE.66: 4 residues within 4Å: Chain L: C.63 Ligands: HAE.49, FE.51, HAE.61 Ligand excluded by PLIP HAE.67: 6 residues within 4Å: Chain D: C.82 Chain L: A.23, C.82 Ligands: HAE.22, FE.23, HAE.45 Ligand excluded by PLIP

24 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: A.1, D.39 Chain C: H.77 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.77, A:D.39, A:D.39 ZN.5: 4 residues within 4Å: Chain A: D.12, H.16 Chain B: H.5, H.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.5, B:H.8, A:D.12, A:H.16 ZN.6: 4 residues within 4Å: Chain A: H.5, H.8 Chain B: D.12, H.16 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.12, B:H.16, A:H.5, A:H.8 ZN.13: 3 residues within 4Å: Chain B: A.1, D.39 Chain F: H.77 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B Metal complexes: F:H.77, B:D.39, B:D.39 ZN.18: 3 residues within 4Å: Chain C: A.1, D.39 Chain D: H.77 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.77, C:D.39, C:D.39 ZN.19: 4 residues within 4Å: Chain C: H.5, H.8 Chain L: D.12, H.16 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain C Metal complexes: L:D.12, L:H.16, C:H.5, C:H.8 ZN.24: 3 residues within 4Å: Chain A: H.77 Chain D: A.1, D.39 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Metal complexes: D:D.39, D:D.39, A:H.77 ZN.25: 4 residues within 4Å: Chain D: D.12, H.16 Chain G: H.5, H.8 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain D Metal complexes: G:H.5, G:H.8, D:D.12, D:H.16 ZN.26: 4 residues within 4Å: Chain D: H.5, H.8 Chain G: D.12, H.16 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain D Metal complexes: G:D.12, G:H.16, D:H.5, D:H.8 ZN.30: 3 residues within 4Å: Chain E: A.1, D.39 Chain G: H.77 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Metal complexes: E:D.39, E:D.39, G:H.77 ZN.31: 4 residues within 4Å: Chain E: D.12, H.16 Chain F: H.5, H.8 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Metal complexes: F:H.5, F:H.8, E:D.12, E:H.16 ZN.32: 4 residues within 4Å: Chain E: H.5, H.8 Chain F: D.12, H.16 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Metal complexes: E:H.5, E:H.8, F:D.12, F:H.16 ZN.37: 3 residues within 4Å: Chain F: A.1, D.39 Chain J: H.77 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain J Metal complexes: F:D.39, F:D.39, J:H.77 ZN.41: 3 residues within 4Å: Chain G: A.1, D.39 Chain H: H.77 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Metal complexes: G:D.39, G:D.39, H:H.77 ZN.46: 3 residues within 4Å: Chain E: H.77 Chain H: A.1, D.39 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain H Metal complexes: E:H.77, H:D.39, H:D.39 ZN.47: 4 residues within 4Å: Chain H: H.5, H.8 Chain K: D.12, H.16 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain K Metal complexes: H:H.5, H:H.8, K:D.12, K:H.16 ZN.52: 3 residues within 4Å: Chain I: A.1, D.39 Chain K: H.77 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I Metal complexes: K:H.77, I:D.39, I:D.39 ZN.53: 4 residues within 4Å: Chain I: H.5, H.8 Chain J: D.12, H.16 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J Metal complexes: I:H.5, I:H.8, J:D.12, J:H.16 ZN.54: 4 residues within 4Å: Chain I: D.12, H.16 Chain J: H.5, H.8 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I Metal complexes: J:H.5, J:H.8, I:D.12, I:H.16 ZN.58: 3 residues within 4Å: Chain B: H.77 Chain J: A.1, D.39 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain J Metal complexes: B:H.77, J:D.39, J:D.39 ZN.59: 4 residues within 4Å: Chain H: D.12, H.16 Chain K: H.5, H.8 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain H Metal complexes: K:H.5, K:H.8, H:D.12, H:H.16 ZN.63: 3 residues within 4Å: Chain K: A.1, D.39 Chain L: H.77 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K Metal complexes: L:H.77, K:D.39, K:D.39 ZN.64: 4 residues within 4Å: Chain C: D.12, H.16 Chain L: H.5, H.8 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain L Metal complexes: C:D.12, C:H.16, L:H.5, L:H.8 ZN.68: 3 residues within 4Å: Chain I: H.77 Chain L: A.1, D.39 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain I Metal complexes: L:D.39, L:D.39, I:H.77

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

FE.7: 3 residues within 4Å: Ligands: HAE.3, HAE.36, HAE.40 No protein-ligand interaction detected (PLIP) FE.11: 3 residues within 4Å: Ligands: HAE.9, HAE.35, HAE.56 No protein-ligand interaction detected (PLIP) FE.12: 3 residues within 4Å: Ligands: HAE.10, HAE.17, HAE.50 No protein-ligand interaction detected (PLIP) FE.14: 3 residues within 4Å: Ligands: HAE.2, HAE.16, HAE.21 No protein-ligand interaction detected (PLIP) FE.23: 3 residues within 4Å: Ligands: HAE.22, HAE.45, HAE.67 No protein-ligand interaction detected (PLIP) FE.33: 3 residues within 4Å: Ligands: HAE.29, HAE.57, HAE.62 No protein-ligand interaction detected (PLIP) FE.42: 3 residues within 4Å: Ligands: HAE.28, HAE.39, HAE.44 No protein-ligand interaction detected (PLIP) FE.51: 3 residues within 4Å: Ligands: HAE.49, HAE.61, HAE.66 No protein-ligand interaction detected (PLIP)

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Soluble cytochrome b562

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