SMTL ID : 6wz3.1

Cu-bound structure of the engineered protein trimer, TriCyt3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 Ligands: CL.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:N.11, A:L.14, A:P.45, A:F.61, A:F.61, A:F.65, A:F.65, A:F.65, A:R.106 Water bridges: A:E.4 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.7: 18 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:N.11, B:L.14, B:P.45, B:F.61, B:F.61, B:F.65, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:L.3 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.10: 20 residues within 4Å: Chain C: L.3, E.4, M.7, E.8, L.10, 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 Ligands: CL.12 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:R.106 Hydrogen bonds: C:E.4 pi-Cation interactions: C:R.106 Metal complexes: C:H.102

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: I.59, R.62 Chain B: I.59, R.62 Chain C: I.59, R.62 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.41 Chain B: K.41 Chain C: K.41 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.34, H.73, A.76 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.106 Ligands: HEC.1 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.34, H.73, A.76 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: R.34, H.73, A.76 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: R.106 Ligands: HEC.10 Ligand excluded by PLIP

1 x CU: COPPER (II) ION(Non-covalent)

CU.6: 6 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Metal complexes: B:H.73, B:H.77, A:H.73, A:H.77, C:H.73, C:H.77

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 4 residues within 4Å: Chain B: N.22, A.23, A.24, V.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.23, B:A.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakkis, A. et al., Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-09-16

Peptides

Soluble cytochrome b562: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Soluble cytochrome b562

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