SMTL ID : 6ot7.1

Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-12-mer

Ligands

12 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 Hydrogen bonds: A:E.4 Salt bridges: A:H.8 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.9: 17 residues within 4Å: Chain B: E.4, M.7, H.8, N.11, 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 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:M.7, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:L.94, B:R.106 Hydrogen bonds: B:E.4 Salt bridges: B:H.8 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.16: 17 residues within 4Å: Chain C: E.4, M.7, H.8, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:E.4, C:M.7, C:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65 Hydrogen bonds: C:E.4 Water bridges: C:E.4, C:E.4, C:R.106 Salt bridges: C:H.8 pi-Stacking: C:F.65, C:H.102 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.20: 17 residues within 4Å: Chain D: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:M.7, D:N.11, D:P.45, D:F.61, D:F.65, D:F.65, D:F.65, D:L.68, D:R.106 Water bridges: D:H.8 Salt bridges: D:H.8 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.25: 18 residues within 4Å: Chain E: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:M.7, E:N.11, E:P.45, E:F.61, E:F.65, E:F.65, E:F.65, E:L.68, E:R.106 Hydrogen bonds: E:E.4 Salt bridges: E:H.8 pi-Cation interactions: E:R.106 Metal complexes: E:H.102 HEC.33: 17 residues within 4Å: Chain F: E.4, M.7, H.8, N.11, 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 13 PLIP interactions: 13 interactions with chain F, Hydrophobic interactions: F:M.7, F:P.45, F:F.61, F:F.65, F:F.65, F:F.65, F:L.68, F:L.94, F:R.106 Hydrogen bonds: F:E.4 Salt bridges: F:H.8 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEC.40: 17 residues within 4Å: Chain G: E.4, M.7, H.8, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain G, Hydrophobic interactions: G:E.4, G:M.7, G:N.11, G:L.14, G:P.45, G:F.61, G:F.65, G:F.65 Hydrogen bonds: G:E.4 Water bridges: G:E.4, G:E.4, G:R.106 Salt bridges: G:H.8 pi-Stacking: G:F.65, G:H.102 pi-Cation interactions: G:R.106 Metal complexes: G:H.102 HEC.44: 17 residues within 4Å: Chain H: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain H, Hydrophobic interactions: H:M.7, H:N.11, H:P.45, H:F.61, H:F.65, H:F.65, H:F.65, H:L.68, H:R.106 Water bridges: H:H.8 Salt bridges: H:H.8 pi-Cation interactions: H:R.106 Metal complexes: H:H.102 HEC.49: 18 residues within 4Å: Chain I: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain I, Hydrophobic interactions: I:M.7, I:N.11, I:P.45, I:F.61, I:F.65, I:F.65, I:F.65, I:L.68, I:R.106 Hydrogen bonds: I:E.4 Salt bridges: I:H.8 pi-Cation interactions: I:R.106 Metal complexes: I:H.102 HEC.57: 17 residues within 4Å: Chain J: E.4, M.7, H.8, N.11, 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 13 PLIP interactions: 13 interactions with chain J, Hydrophobic interactions: J:M.7, J:P.45, J:F.61, J:F.65, J:F.65, J:F.65, J:L.68, J:L.94, J:R.106 Hydrogen bonds: J:E.4 Salt bridges: J:H.8 pi-Cation interactions: J:R.106 Metal complexes: J:H.102 HEC.64: 17 residues within 4Å: Chain K: E.4, M.7, H.8, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain K, Hydrophobic interactions: K:E.4, K:M.7, K:N.11, K:L.14, K:P.45, K:F.61, K:F.65, K:F.65 Hydrogen bonds: K:E.4 Water bridges: K:E.4, K:E.4, K:R.106 Salt bridges: K:H.8 pi-Stacking: K:F.65, K:H.102 pi-Cation interactions: K:R.106 Metal complexes: K:H.102 HEC.68: 17 residues within 4Å: Chain L: E.4, M.7, H.8, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain L, Hydrophobic interactions: L:M.7, L:N.11, L:P.45, L:F.61, L:F.65, L:F.65, L:F.65, L:L.68, L:R.106 Water bridges: L:H.8 Salt bridges: L:H.8 pi-Cation interactions: L:R.106 Metal complexes: L:H.102

21 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.12, H.16 Chain H: H.5, H.8 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain A Metal complexes: H:H.5, H:H.8, A:D.12, A:D.12, A:H.16 ZN.3: 3 residues within 4Å: Chain A: A.1, D.39 Chain B: H.77 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.77, A:A.1, A:D.39, A:D.39, H2O.2 ZN.8: 3 residues within 4Å: Chain A: H.77 Chain D: A.1, D.39 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.77, D:A.1, D:D.39, D:D.39, H2O.12 ZN.10: 3 residues within 4Å: Chain B: A.1, D.39 Chain D: H.77 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:A.1, B:D.39, B:D.39, D:H.77, H2O.5 ZN.13: 4 residues within 4Å: Chain B: H.5, H.8 Chain C: D.12, H.16 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.5, B:H.8, C:D.12, C:D.12, C:H.16 ZN.15: 4 residues within 4Å: Chain B: D.12, H.16 Chain C: H.5, H.8 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Metal complexes: C:H.5, C:H.8, B:D.12, B:D.12, B:H.16 ZN.21: 4 residues within 4Å: Chain D: D.12, H.16 Chain I: H.5, H.8 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain D Metal complexes: I:H.5, I:H.8, D:D.12, D:D.12, D:H.16 ZN.26: 4 residues within 4Å: Chain E: D.12, H.16 Chain L: H.5, H.8 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain E Metal complexes: L:H.5, L:H.8, E:D.12, E:D.12, E:H.16 ZN.27: 3 residues within 4Å: Chain E: A.1, D.39 Chain F: H.77 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:A.1, E:D.39, E:D.39, F:H.77, H2O.15 ZN.32: 3 residues within 4Å: Chain E: H.77 Chain H: A.1, D.39 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: H:A.1, H:D.39, H:D.39, E:H.77, H2O.25 ZN.34: 3 residues within 4Å: Chain F: A.1, D.39 Chain H: H.77 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: F:A.1, F:D.39, F:D.39, H:H.77, H2O.18 ZN.37: 4 residues within 4Å: Chain F: H.5, H.8 Chain G: D.12, H.16 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F Metal complexes: G:D.12, G:D.12, G:H.16, F:H.5, F:H.8 ZN.39: 4 residues within 4Å: Chain F: D.12, H.16 Chain G: H.5, H.8 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain F Metal complexes: G:H.5, G:H.8, F:D.12, F:D.12, F:H.16 ZN.45: 4 residues within 4Å: Chain A: H.5, H.8 Chain H: D.12, H.16 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain A Metal complexes: H:D.12, H:D.12, H:H.16, A:H.5, A:H.8 ZN.50: 4 residues within 4Å: Chain D: H.5, H.8 Chain I: D.12, H.16 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain D Metal complexes: I:D.12, I:D.12, I:H.16, D:H.5, D:H.8 ZN.51: 3 residues within 4Å: Chain I: A.1, D.39 Chain J: H.77 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:A.1, I:D.39, I:D.39, J:H.77, H2O.28 ZN.56: 3 residues within 4Å: Chain I: H.77 Chain L: A.1, D.39 5 PLIP interactions: 1 interactions with chain I, 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: I:H.77, L:A.1, L:D.39, L:D.39, H2O.38 ZN.58: 3 residues within 4Å: Chain J: A.1, D.39 Chain L: H.77 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: J:A.1, J:D.39, J:D.39, L:H.77, H2O.32 ZN.61: 4 residues within 4Å: Chain J: H.5, H.8 Chain K: D.12, H.16 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain K Metal complexes: J:H.5, J:H.8, K:D.12, K:D.12, K:H.16 ZN.63: 4 residues within 4Å: Chain J: D.12, H.16 Chain K: H.5, H.8 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain K Metal complexes: J:D.12, J:D.12, J:H.16, K:H.5, K:H.8 ZN.69: 4 residues within 4Å: Chain E: H.5, H.8 Chain L: D.12, H.16 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain E Metal complexes: L:D.12, L:D.12, L:H.16, E:H.5, E:H.8

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

FE.4: 5 residues within 4Å: Ligands: HAE.6, FE.28, HAE.30, FE.52, HAE.54 No protein-ligand interaction detected (PLIP) FE.7: 3 residues within 4Å: Ligands: HAE.5, HAE.11, HAE.22 No protein-ligand interaction detected (PLIP) FE.14: 3 residues within 4Å: Ligands: HAE.18, HAE.23, HAE.60 No protein-ligand interaction detected (PLIP) FE.17: 5 residues within 4Å: Ligands: HAE.19, FE.41, HAE.43, FE.65, HAE.67 No protein-ligand interaction detected (PLIP) FE.28: 5 residues within 4Å: Ligands: FE.4, HAE.6, HAE.30, FE.52, HAE.54 No protein-ligand interaction detected (PLIP) FE.31: 3 residues within 4Å: Ligands: HAE.29, HAE.35, HAE.46 No protein-ligand interaction detected (PLIP) FE.38: 3 residues within 4Å: Ligands: HAE.12, HAE.42, HAE.47 No protein-ligand interaction detected (PLIP) FE.41: 5 residues within 4Å: Ligands: FE.17, HAE.19, HAE.43, FE.65, HAE.67 No protein-ligand interaction detected (PLIP) FE.52: 5 residues within 4Å: Ligands: FE.4, HAE.6, FE.28, HAE.30, HAE.54 No protein-ligand interaction detected (PLIP) FE.55: 3 residues within 4Å: Ligands: HAE.53, HAE.59, HAE.70 No protein-ligand interaction detected (PLIP) FE.62: 3 residues within 4Å: Ligands: HAE.36, HAE.66, HAE.71 No protein-ligand interaction detected (PLIP) FE.65: 5 residues within 4Å: Ligands: FE.17, HAE.19, FE.41, HAE.43, HAE.67 No protein-ligand interaction detected (PLIP)

24 x HAE: ACETOHYDROXAMIC ACID(Covalent)

HAE.5: 6 residues within 4Å: Chain A: C.63, W.66 Chain D: S.59 Ligands: FE.7, HAE.11, HAE.22 Ligand excluded by PLIP HAE.6: 10 residues within 4Å: Chain A: A.23, A.79, K.80, C.82 Chain I: T.24 Ligands: FE.4, FE.28, HAE.30, FE.52, HAE.54 Ligand excluded by PLIP HAE.11: 6 residues within 4Å: Chain A: S.59 Chain B: C.63, W.66 Ligands: HAE.5, FE.7, HAE.22 Ligand excluded by PLIP HAE.12: 6 residues within 4Å: Chain B: A.23, K.27, C.82 Ligands: FE.38, HAE.42, HAE.47 Ligand excluded by PLIP HAE.18: 8 residues within 4Å: Chain C: K.27, A.79, K.80, C.82 Chain J: T.24 Ligands: FE.14, HAE.23, HAE.60 Ligand excluded by PLIP HAE.19: 6 residues within 4Å: Chain C: C.63 Ligands: FE.17, FE.41, HAE.43, FE.65, HAE.67 Ligand excluded by PLIP HAE.22: 5 residues within 4Å: Chain B: S.59 Chain D: C.63 Ligands: HAE.5, FE.7, HAE.11 Ligand excluded by PLIP HAE.23: 6 residues within 4Å: Chain D: A.23, C.82 Chain J: C.82 Ligands: FE.14, HAE.18, HAE.60 Ligand excluded by PLIP HAE.29: 6 residues within 4Å: Chain E: C.63, W.66 Chain H: S.59 Ligands: FE.31, HAE.35, HAE.46 Ligand excluded by PLIP HAE.30: 10 residues within 4Å: Chain A: T.24 Chain E: A.23, A.79, K.80, C.82 Ligands: FE.4, HAE.6, FE.28, FE.52, HAE.54 Ligand excluded by PLIP HAE.35: 6 residues within 4Å: Chain E: S.59 Chain F: C.63, W.66 Ligands: HAE.29, FE.31, HAE.46 Ligand excluded by PLIP HAE.36: 6 residues within 4Å: Chain F: A.23, K.27, C.82 Ligands: FE.62, HAE.66, HAE.71 Ligand excluded by PLIP HAE.42: 8 residues within 4Å: Chain B: T.24 Chain G: K.27, A.79, K.80, C.82 Ligands: HAE.12, FE.38, HAE.47 Ligand excluded by PLIP HAE.43: 6 residues within 4Å: Chain G: C.63 Ligands: FE.17, HAE.19, FE.41, FE.65, HAE.67 Ligand excluded by PLIP HAE.46: 5 residues within 4Å: Chain F: S.59 Chain H: C.63 Ligands: HAE.29, FE.31, HAE.35 Ligand excluded by PLIP HAE.47: 6 residues within 4Å: Chain B: C.82 Chain H: A.23, C.82 Ligands: HAE.12, FE.38, HAE.42 Ligand excluded by PLIP HAE.53: 6 residues within 4Å: Chain I: C.63, W.66 Chain L: S.59 Ligands: FE.55, HAE.59, HAE.70 Ligand excluded by PLIP HAE.54: 10 residues within 4Å: Chain E: T.24 Chain I: A.23, A.79, K.80, C.82 Ligands: FE.4, HAE.6, FE.28, HAE.30, FE.52 Ligand excluded by PLIP HAE.59: 6 residues within 4Å: Chain I: S.59 Chain J: C.63, W.66 Ligands: HAE.53, FE.55, HAE.70 Ligand excluded by PLIP HAE.60: 6 residues within 4Å: Chain J: A.23, K.27, C.82 Ligands: FE.14, HAE.18, HAE.23 Ligand excluded by PLIP HAE.66: 8 residues within 4Å: Chain F: T.24 Chain K: K.27, A.79, K.80, C.82 Ligands: HAE.36, FE.62, HAE.71 Ligand excluded by PLIP HAE.67: 6 residues within 4Å: Chain K: C.63 Ligands: FE.17, HAE.19, FE.41, HAE.43, FE.65 Ligand excluded by PLIP HAE.70: 5 residues within 4Å: Chain J: S.59 Chain L: C.63 Ligands: HAE.53, FE.55, HAE.59 Ligand excluded by PLIP HAE.71: 6 residues within 4Å: Chain F: C.82 Chain L: A.23, C.82 Ligands: HAE.36, FE.62, HAE.66 Ligand excluded by PLIP

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.24: 12 residues within 4Å: Chain A: Q.38, W.41, W.66, I.69 Chain B: Q.38, W.41, W.66, I.69 Chain D: Q.38, W.41, W.66, I.69 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:Q.38, B:Q.38, A:Q.38 1PE.48: 12 residues within 4Å: Chain E: Q.38, W.41, W.66, I.69 Chain F: Q.38, W.41, W.66, I.69 Chain H: Q.38, W.41, W.66, I.69 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain H Hydrogen bonds: E:Q.38, F:Q.38, H:Q.38 1PE.72: 12 residues within 4Å: Chain I: Q.38, W.41, W.66, I.69 Chain J: Q.38, W.41, W.66, I.69 Chain L: Q.38, W.41, W.66, I.69 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I, 1 interactions with chain L Hydrogen bonds: J:Q.38, I:Q.38, L:Q.38

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
D

B
A

C
B

D
C

E
D

F
A

G
B

H
C

I
D

J
A

K
B

L
C

Soluble cytochrome b562

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