SMTL ID : 6ot4.1

Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-12-mer

Ligands

12 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 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:L.68, A:R.106 Water bridges: A:E.4, A:E.4, A:R.106 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.8: 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 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:N.11, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Water bridges: B:E.4, B:R.106 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.14: 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 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:M.7, C:N.11, C:P.45, C:F.61, C:F.61, C:F.65, C:F.65, C:F.65, C:L.68, C:L.94, C:R.106 Water bridges: C:R.106 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 14 PLIP interactions: 14 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:L.68, D:L.68, D:R.106 Water bridges: D:R.106, D:R.106 pi-Stacking: D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.23: 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 16 PLIP interactions: 16 interactions with chain E, Hydrophobic interactions: E:M.7, E:L.10, E:N.11, E:L.14, E:P.45, E:F.61, E:F.65, E:F.65, E:L.68, E:R.106 Water bridges: E:E.4, E:E.4, E:R.106 pi-Stacking: E:H.102 pi-Cation interactions: E:R.106 Metal complexes: E:H.102 HEC.30: 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 15 PLIP interactions: 15 interactions with chain F, Hydrophobic interactions: F:M.7, F:L.10, F:N.11, F:L.14, F:P.45, F:F.61, F:F.65, F:F.65, F:F.65, F:L.68, F:R.106 Water bridges: F:E.4, F:R.106 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEC.36: 21 residues within 4Å: Chain G: 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 14 PLIP interactions: 14 interactions with chain G, Hydrophobic interactions: G:M.7, G:N.11, G:P.45, G:F.61, G:F.61, G:F.65, G:F.65, G:F.65, G:L.68, G:L.94, G:R.106 Water bridges: G:R.106 pi-Cation interactions: G:R.106 Metal complexes: G:H.102 HEC.41: 21 residues within 4Å: Chain H: 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 14 PLIP interactions: 14 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:L.68, H:L.68, H:R.106 Water bridges: H:R.106, H:R.106 pi-Stacking: H:H.102 pi-Cation interactions: H:R.106 Metal complexes: H:H.102 HEC.45: 21 residues within 4Å: Chain I: 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 16 PLIP interactions: 16 interactions with chain I, Hydrophobic interactions: I:M.7, I:L.10, I:N.11, I:L.14, I:P.45, I:F.61, I:F.65, I:F.65, I:L.68, I:R.106 Water bridges: I:E.4, I:E.4, I:R.106 pi-Stacking: I:H.102 pi-Cation interactions: I:R.106 Metal complexes: I:H.102 HEC.52: 21 residues within 4Å: Chain J: 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 15 PLIP interactions: 15 interactions with chain J, Hydrophobic interactions: J:M.7, J:L.10, J:N.11, J:L.14, J:P.45, J:F.61, J:F.65, J:F.65, J:F.65, J:L.68, J:R.106 Water bridges: J:E.4, J:R.106 pi-Cation interactions: J:R.106 Metal complexes: J:H.102 HEC.58: 21 residues within 4Å: Chain K: 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 14 PLIP interactions: 14 interactions with chain K, Hydrophobic interactions: K:M.7, K:N.11, K:P.45, K:F.61, K:F.61, K:F.65, K:F.65, K:F.65, K:L.68, K:L.94, K:R.106 Water bridges: K:R.106 pi-Cation interactions: K:R.106 Metal complexes: K:H.102 HEC.63: 21 residues within 4Å: Chain L: 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 14 PLIP interactions: 14 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:L.68, L:L.68, L:R.106 Water bridges: L:R.106, L:R.106 pi-Stacking: L:H.102 pi-Cation interactions: L:R.106 Metal complexes: L:H.102

24 x HAE: ACETOHYDROXAMIC ACID(Covalent)

HAE.2: 6 residues within 4Å: Chain A: C.63, W.66 Chain D: W.66 Ligands: FE.4, HAE.15, HAE.20 Ligand excluded by PLIP HAE.3: 9 residues within 4Å: Chain A: A.23, K.27, A.79, K.80, C.82 Chain K: T.24 Ligands: HAE.54, FE.57, HAE.60 Ligand excluded by PLIP HAE.9: 9 residues within 4Å: Chain B: C.63, W.66, E.67 Chain F: W.66 Ligands: FE.11, HAE.31, FE.33, HAE.53, FE.55 Ligand excluded by PLIP HAE.10: 10 residues within 4Å: Chain B: A.23, K.27, A.79, K.80, Q.81, C.82 Chain E: T.24 Ligands: FE.13, HAE.16, HAE.25 Ligand excluded by PLIP HAE.15: 6 residues within 4Å: Chain A: W.66 Chain C: C.63, W.66 Ligands: HAE.2, FE.4, HAE.20 Ligand excluded by PLIP HAE.16: 10 residues within 4Å: Chain B: T.24 Chain C: A.23, K.27, A.79, K.80, Q.81, C.82 Ligands: HAE.10, FE.13, HAE.25 Ligand excluded by PLIP HAE.20: 6 residues within 4Å: Chain C: W.66 Chain D: C.63, W.66 Ligands: HAE.2, FE.4, HAE.15 Ligand excluded by PLIP HAE.21: 11 residues within 4Å: Chain D: A.23, K.27, A.79, K.80, C.82 Chain H: T.24 Ligands: FE.22, HAE.43, FE.44, HAE.65, FE.66 Ligand excluded by PLIP HAE.24: 6 residues within 4Å: Chain E: C.63, W.66 Chain H: W.66 Ligands: FE.26, HAE.37, HAE.42 Ligand excluded by PLIP HAE.25: 9 residues within 4Å: Chain C: T.24 Chain E: A.23, K.27, A.79, K.80, C.82 Ligands: HAE.10, FE.13, HAE.16 Ligand excluded by PLIP HAE.31: 9 residues within 4Å: Chain F: C.63, W.66, E.67 Chain J: W.66 Ligands: HAE.9, FE.11, FE.33, HAE.53, FE.55 Ligand excluded by PLIP HAE.32: 10 residues within 4Å: Chain F: A.23, K.27, A.79, K.80, Q.81, C.82 Chain I: T.24 Ligands: FE.35, HAE.38, HAE.47 Ligand excluded by PLIP HAE.37: 6 residues within 4Å: Chain E: W.66 Chain G: C.63, W.66 Ligands: HAE.24, FE.26, HAE.42 Ligand excluded by PLIP HAE.38: 10 residues within 4Å: Chain F: T.24 Chain G: A.23, K.27, A.79, K.80, Q.81, C.82 Ligands: HAE.32, FE.35, HAE.47 Ligand excluded by PLIP HAE.42: 6 residues within 4Å: Chain G: W.66 Chain H: C.63, W.66 Ligands: HAE.24, FE.26, HAE.37 Ligand excluded by PLIP HAE.43: 11 residues within 4Å: Chain H: A.23, K.27, A.79, K.80, C.82 Chain L: T.24 Ligands: HAE.21, FE.22, FE.44, HAE.65, FE.66 Ligand excluded by PLIP HAE.46: 6 residues within 4Å: Chain I: C.63, W.66 Chain L: W.66 Ligands: FE.48, HAE.59, HAE.64 Ligand excluded by PLIP HAE.47: 9 residues within 4Å: Chain G: T.24 Chain I: A.23, K.27, A.79, K.80, C.82 Ligands: HAE.32, FE.35, HAE.38 Ligand excluded by PLIP HAE.53: 9 residues within 4Å: Chain B: W.66 Chain J: C.63, W.66, E.67 Ligands: HAE.9, FE.11, HAE.31, FE.33, FE.55 Ligand excluded by PLIP HAE.54: 10 residues within 4Å: Chain A: T.24 Chain J: A.23, K.27, A.79, K.80, Q.81, C.82 Ligands: HAE.3, FE.57, HAE.60 Ligand excluded by PLIP HAE.59: 6 residues within 4Å: Chain I: W.66 Chain K: C.63, W.66 Ligands: HAE.46, FE.48, HAE.64 Ligand excluded by PLIP HAE.60: 10 residues within 4Å: Chain J: T.24 Chain K: A.23, K.27, A.79, K.80, Q.81, C.82 Ligands: HAE.3, HAE.54, FE.57 Ligand excluded by PLIP HAE.64: 6 residues within 4Å: Chain K: W.66 Chain L: C.63, W.66 Ligands: HAE.46, FE.48, HAE.59 Ligand excluded by PLIP HAE.65: 11 residues within 4Å: Chain D: T.24 Chain L: A.23, K.27, A.79, K.80, C.82 Ligands: HAE.21, FE.22, HAE.43, FE.44, FE.66 Ligand excluded by PLIP

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

FE.4: 3 residues within 4Å: Ligands: HAE.2, HAE.15, HAE.20 No protein-ligand interaction detected (PLIP) FE.11: 8 residues within 4Å: Chain B: W.66 Chain F: W.66 Chain J: W.66 Ligands: HAE.9, HAE.31, FE.33, HAE.53, FE.55 No protein-ligand interaction detected (PLIP) FE.13: 3 residues within 4Å: Ligands: HAE.10, HAE.16, HAE.25 No protein-ligand interaction detected (PLIP) FE.22: 5 residues within 4Å: Ligands: HAE.21, HAE.43, FE.44, HAE.65, FE.66 No protein-ligand interaction detected (PLIP) FE.26: 3 residues within 4Å: Ligands: HAE.24, HAE.37, HAE.42 No protein-ligand interaction detected (PLIP) FE.33: 8 residues within 4Å: Chain B: W.66 Chain F: W.66 Chain J: W.66 Ligands: HAE.9, FE.11, HAE.31, HAE.53, FE.55 No protein-ligand interaction detected (PLIP) FE.35: 3 residues within 4Å: Ligands: HAE.32, HAE.38, HAE.47 No protein-ligand interaction detected (PLIP) FE.44: 5 residues within 4Å: Ligands: HAE.21, FE.22, HAE.43, HAE.65, FE.66 No protein-ligand interaction detected (PLIP) FE.48: 3 residues within 4Å: Ligands: HAE.46, HAE.59, HAE.64 No protein-ligand interaction detected (PLIP) FE.55: 8 residues within 4Å: Chain B: W.66 Chain F: W.66 Chain J: W.66 Ligands: HAE.9, FE.11, HAE.31, FE.33, HAE.53 No protein-ligand interaction detected (PLIP) FE.57: 3 residues within 4Å: Ligands: HAE.3, HAE.54, HAE.60 No protein-ligand interaction detected (PLIP) FE.66: 5 residues within 4Å: Ligands: HAE.21, FE.22, HAE.43, FE.44, HAE.65 No protein-ligand interaction detected (PLIP)

18 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: A.1, N.6, D.39 Chain C: H.77 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:A.1, A:D.39, C:H.77, H2O.21 ZN.6: 4 residues within 4Å: Chain A: H.8, D.12 Chain B: H.8, D.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.8, A:D.12, A:D.12, B:H.8, B:D.12 ZN.7: 4 residues within 4Å: Chain A: H.77 Chain D: A.1, N.6, 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.28 ZN.12: 4 residues within 4Å: Chain B: A.1, N.6, D.39 Chain J: H.77 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: B:A.1, B:D.39, J:H.77, H2O.13 ZN.17: 4 residues within 4Å: Chain C: A.1, N.6, D.39 Chain D: H.77 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:A.1, C:D.39, D:H.77, H2O.21 ZN.18: 4 residues within 4Å: Chain C: H.8, D.12 Chain H: H.8, D.12 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain C Metal complexes: H:H.8, H:D.12, C:H.8, C:D.12, C:D.12 ZN.27: 4 residues within 4Å: Chain E: A.1, N.6, D.39 Chain G: H.77 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:A.1, E:D.39, G:H.77, H2O.51 ZN.28: 4 residues within 4Å: Chain E: H.8, D.12 Chain F: H.8, D.12 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Metal complexes: E:H.8, E:D.12, E:D.12, F:H.8, F:D.12 ZN.29: 4 residues within 4Å: Chain E: H.77 Chain H: A.1, N.6, 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.58 ZN.34: 4 residues within 4Å: Chain B: H.77 Chain F: A.1, N.6, D.39 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.77, F:A.1, F:D.39, H2O.43 ZN.39: 4 residues within 4Å: Chain G: A.1, N.6, D.39 Chain H: H.77 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:A.1, G:D.39, H:H.77, H2O.51 ZN.40: 4 residues within 4Å: Chain G: H.8, D.12 Chain L: H.8, D.12 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain G Metal complexes: L:H.8, L:D.12, G:H.8, G:D.12, G:D.12 ZN.49: 4 residues within 4Å: Chain I: A.1, N.6, D.39 Chain K: H.77 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: I:A.1, I:D.39, K:H.77, H2O.81 ZN.50: 4 residues within 4Å: Chain I: H.8, D.12 Chain J: H.8, D.12 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J Metal complexes: I:H.8, I:D.12, I:D.12, J:H.8, J:D.12 ZN.51: 4 residues within 4Å: Chain I: H.77 Chain L: A.1, N.6, 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.88 ZN.56: 4 residues within 4Å: Chain F: H.77 Chain J: A.1, N.6, D.39 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: F:H.77, J:A.1, J:D.39, H2O.73 ZN.61: 4 residues within 4Å: Chain K: A.1, N.6, D.39 Chain L: H.77 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:A.1, K:D.39, L:H.77, H2O.81 ZN.62: 4 residues within 4Å: Chain D: H.8, D.12 Chain K: H.8, D.12 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain K Metal complexes: D:H.8, D:D.12, K:H.8, K:D.12, K:D.12

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
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Soluble cytochrome b562