SMTL ID : 6ot9.1

Bimetallic dodecameric cage design 1 (BMC1) from cytochrome cb562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

18 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: A.1, D.39 Chain B: H.77 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.77, A:A.1, A:D.39, A:D.39 ZN.2: 4 residues within 4Å: Chain A: H.8, D.12 Chain J: H.8, D.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain J Metal complexes: A:H.8, A:D.12, A:D.12, J:H.8, J:D.12 ZN.5: 3 residues within 4Å: Chain A: H.77 Chain D: A.1, D.39 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.77, D:A.1, D:D.39 ZN.7: 3 residues within 4Å: Chain B: A.1, D.39 Chain D: H.77 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.77, B:A.1, B:D.39 ZN.10: 3 residues within 4Å: Chain C: A.1, D.39 Chain G: H.77 4 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: G:H.77, C:A.1, C:D.39, H2O.1 ZN.14: 4 residues within 4Å: Chain C: H.8, D.12 Chain D: H.8, D.12 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.8, D:D.12, D:D.12, C:H.8, C:D.12 ZN.17: 3 residues within 4Å: Chain E: A.1, D.39 Chain F: H.77 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:A.1, E:D.39, E:D.39, F:H.77 ZN.18: 4 residues within 4Å: Chain B: H.8, D.12 Chain E: H.8, D.12 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Metal complexes: E:H.8, E:D.12, E:D.12, B:H.8, B:D.12 ZN.21: 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:A.1, H:D.39 ZN.23: 3 residues within 4Å: Chain F: A.1, D.39 Chain H: H.77 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain F Metal complexes: H:H.77, F:A.1, F:D.39 ZN.26: 3 residues within 4Å: Chain G: A.1, D.39 Chain K: H.77 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: G:A.1, G:D.39, K:H.77, H2O.2 ZN.30: 4 residues within 4Å: Chain G: H.8, D.12 Chain H: H.8, D.12 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain H Metal complexes: G:H.8, G:D.12, H:H.8, H:D.12, H:D.12 ZN.33: 3 residues within 4Å: Chain I: A.1, D.39 Chain J: H.77 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J Metal complexes: I:A.1, I:D.39, I:D.39, J:H.77 ZN.34: 4 residues within 4Å: Chain F: H.8, D.12 Chain I: H.8, D.12 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain I Metal complexes: F:H.8, F:D.12, I:H.8, I:D.12, I:D.12 ZN.37: 3 residues within 4Å: Chain I: H.77 Chain L: A.1, D.39 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain L Metal complexes: I:H.77, L:A.1, L:D.39 ZN.39: 3 residues within 4Å: Chain J: A.1, D.39 Chain L: H.77 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain J Metal complexes: L:H.77, J:A.1, J:D.39 ZN.42: 3 residues within 4Å: Chain C: H.77 Chain K: A.1, D.39 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: C:H.77, K:A.1, K:D.39, H2O.2 ZN.46: 4 residues within 4Å: Chain K: H.8, D.12 Chain L: H.8, D.12 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L Metal complexes: K:H.8, K:D.12, L:H.8, L:D.12, L:D.12

12 x HAE: ACETOHYDROXAMIC ACID(Covalent)

HAE.3: 7 residues within 4Å: Chain A: C.63, E.67 Chain D: S.59, W.66 Ligands: FE.6, HAE.8, HAE.15 No protein-ligand interaction detected (PLIP) HAE.8: 4 residues within 4Å: Chain B: C.63 Ligands: HAE.3, FE.6, HAE.15 No protein-ligand interaction detected (PLIP) HAE.12: 7 residues within 4Å: Chain C: C.63 Chain K: S.59 Ligands: FE.11, FE.27, HAE.28, FE.43, HAE.44 No protein-ligand interaction detected (PLIP) HAE.15: 5 residues within 4Å: Chain B: S.59 Chain D: C.63 Ligands: HAE.3, FE.6, HAE.8 No protein-ligand interaction detected (PLIP) HAE.19: 7 residues within 4Å: Chain E: C.63, E.67 Chain H: S.59, W.66 Ligands: FE.22, HAE.24, HAE.31 No protein-ligand interaction detected (PLIP) HAE.24: 4 residues within 4Å: Chain F: C.63 Ligands: HAE.19, FE.22, HAE.31 No protein-ligand interaction detected (PLIP) HAE.28: 7 residues within 4Å: Chain C: S.59 Chain G: C.63 Ligands: FE.11, HAE.12, FE.27, FE.43, HAE.44 No protein-ligand interaction detected (PLIP) HAE.31: 5 residues within 4Å: Chain F: S.59 Chain H: C.63 Ligands: HAE.19, FE.22, HAE.24 No protein-ligand interaction detected (PLIP) HAE.35: 7 residues within 4Å: Chain I: C.63, E.67 Chain L: S.59, W.66 Ligands: FE.38, HAE.40, HAE.47 No protein-ligand interaction detected (PLIP) HAE.40: 4 residues within 4Å: Chain J: C.63 Ligands: HAE.35, FE.38, HAE.47 No protein-ligand interaction detected (PLIP) HAE.44: 7 residues within 4Å: Chain G: S.59 Chain K: C.63 Ligands: FE.11, HAE.12, FE.27, HAE.28, FE.43 No protein-ligand interaction detected (PLIP) HAE.47: 5 residues within 4Å: Chain J: S.59 Chain L: C.63 Ligands: HAE.35, FE.38, HAE.40 No protein-ligand interaction detected (PLIP)

12 x HEC: HEME C(Covalent)

HEC.4: 17 residues within 4Å: Chain A: E.4, M.7, N.11, L.14, 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 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:M.7, A:P.45, A:F.65, A:L.68, A:T.97, A:R.106, A:R.106 Hydrogen bonds: A:E.4 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.9: 16 residues within 4Å: Chain B: L.3, E.4, M.7, N.11, L.14, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:L.3, B:E.4, B:M.7, B:P.45 Hydrogen bonds: B:E.4 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.13: 17 residues within 4Å: Chain C: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, L.94, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:L.10, C:L.10, C:N.11, C:L.14, C:P.45, C:F.61, C:F.61, C:L.94, C:R.106 Metal complexes: C:H.102 HEC.16: 16 residues within 4Å: Chain D: E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:M.7, D:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:L.68, D:R.106 Hydrogen bonds: D:E.4, D:E.4 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEC.20: 17 residues within 4Å: Chain E: E.4, M.7, N.11, L.14, 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 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:M.7, E:P.45, E:F.65, E:L.68, E:T.97, E:R.106, E:R.106 Hydrogen bonds: E:E.4 pi-Cation interactions: E:R.106 Metal complexes: E:H.102 HEC.25: 16 residues within 4Å: Chain F: L.3, E.4, M.7, N.11, L.14, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:L.3, F:E.4, F:M.7, F:P.45 Hydrogen bonds: F:E.4 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEC.29: 17 residues within 4Å: Chain G: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, L.94, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:L.3, G:M.7, G:L.10, G:L.10, G:N.11, G:L.14, G:P.45, G:F.61, G:F.61, G:L.94, G:R.106 Metal complexes: G:H.102 HEC.32: 16 residues within 4Å: Chain H: E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain H, Hydrophobic interactions: H:M.7, H:N.11, H:L.14, H:P.45, H:F.65, H:F.65, H:L.68, H:R.106 Hydrogen bonds: H:E.4, H:E.4 pi-Cation interactions: H:R.106 Metal complexes: H:H.102 HEC.36: 17 residues within 4Å: Chain I: E.4, M.7, N.11, L.14, 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 10 PLIP interactions: 10 interactions with chain I, Hydrophobic interactions: I:M.7, I:P.45, I:F.65, I:L.68, I:T.97, I:R.106, I:R.106 Hydrogen bonds: I:E.4 pi-Cation interactions: I:R.106 Metal complexes: I:H.102 HEC.41: 16 residues within 4Å: Chain J: L.3, E.4, M.7, N.11, L.14, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 7 PLIP interactions: 7 interactions with chain J, Hydrophobic interactions: J:L.3, J:E.4, J:M.7, J:P.45 Hydrogen bonds: J:E.4 pi-Cation interactions: J:R.106 Metal complexes: J:H.102 HEC.45: 17 residues within 4Å: Chain K: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, L.94, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain K, Hydrophobic interactions: K:L.3, K:M.7, K:L.10, K:L.10, K:N.11, K:L.14, K:P.45, K:F.61, K:F.61, K:L.94, K:R.106 Metal complexes: K:H.102 HEC.48: 16 residues within 4Å: Chain L: E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain L, Hydrophobic interactions: L:M.7, L:N.11, L:L.14, L:P.45, L:F.65, L:F.65, L:L.68, L:R.106 Hydrogen bonds: L:E.4, L:E.4 pi-Cation interactions: L:R.106 Metal complexes: L:H.102

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

FE.6: 3 residues within 4Å: Ligands: HAE.3, HAE.8, HAE.15 3 PLIP interactions: 3 Ligand-Ligand interactions Metal complexes: HAE.3, HAE.8, HAE.15 FE.11: 5 residues within 4Å: Ligands: HAE.12, FE.27, HAE.28, FE.43, HAE.44 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: HAE.12 FE.22: 3 residues within 4Å: Ligands: HAE.19, HAE.24, HAE.31 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.19, HAE.24 FE.27: 5 residues within 4Å: Ligands: FE.11, HAE.12, HAE.28, FE.43, HAE.44 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: HAE.28 FE.38: 3 residues within 4Å: Ligands: HAE.35, HAE.40, HAE.47 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HAE.35, HAE.40 FE.43: 5 residues within 4Å: Ligands: FE.11, HAE.12, FE.27, HAE.28, HAE.44 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: HAE.44

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
C

B
D

C
B

D
A

E
C

F
D

G
B

H
A

I
C

J
D

K
B

L
A

Soluble cytochrome b562