SMTL ID : 6wzc.1

Ni-bound structure of an engineered protein trimer, TriCyt3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: 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: CA.7 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:L.14, A:P.45, A:F.65, A:F.65, A:F.65, A:R.106 pi-Cation interactions: A:R.106, A:R.106 Metal complexes: A:H.102 HEC.11: 18 residues within 4Å: Chain B: 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: CA.17 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:M.7, B:N.11, B:L.14, B:P.45, B:F.65, B:F.65, B:F.65, B:R.106 Water bridges: B:E.4, B:E.4 pi-Cation interactions: B:R.106, B:R.106 Metal complexes: B:H.102 HEC.21: 18 residues within 4Å: Chain C: 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: CA.27 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:M.7, C:N.11, C:L.14, C:P.45, C:F.65, C:F.65, C:F.65, C:R.106 pi-Cation interactions: C:R.106, C:R.106 Metal complexes: C:H.102

6 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: A.1, D.39 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.1, A:D.39, H2O.1, H2O.3, H2O.3 NI.3: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.13, NI.23 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.73, B:H.77, C:H.73, C:H.77, A:H.77 NI.12: 2 residues within 4Å: Chain B: A.1, D.39 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.1, B:D.39, H2O.5, H2O.7, H2O.7 NI.13: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.3, NI.23 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.73, B:H.77, C:H.73, C:H.77, A:H.77 NI.22: 2 residues within 4Å: Chain C: A.1, D.39 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.1, C:D.39, H2O.9, H2O.11, H2O.11 NI.23: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.3, NI.13 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Metal complexes: C:H.73, C:H.77, A:H.77, B:H.73, B:H.77

12 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: K.19, D.21 Ligands: CA.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.19, A:D.21, H2O.3 CA.5: 2 residues within 4Å: Chain A: K.19 Ligands: CA.4 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.4 Ligands: CA.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.4, H2O.4 CA.7: 3 residues within 4Å: Chain A: E.4 Ligands: HEC.1, CA.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.4 CA.14: 3 residues within 4Å: Chain B: K.19, D.21 Ligands: CA.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.19, B:D.21, H2O.7 CA.15: 2 residues within 4Å: Chain B: K.19 Ligands: CA.14 No protein-ligand interaction detected (PLIP) CA.16: 2 residues within 4Å: Chain B: E.4 Ligands: CA.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.4, H2O.8 CA.17: 3 residues within 4Å: Chain B: E.4 Ligands: HEC.11, CA.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.4 CA.24: 3 residues within 4Å: Chain C: K.19, D.21 Ligands: CA.25 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.19, C:D.21, H2O.11 CA.25: 2 residues within 4Å: Chain C: K.19 Ligands: CA.24 No protein-ligand interaction detected (PLIP) CA.26: 2 residues within 4Å: Chain C: E.4 Ligands: CA.27 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.4, H2O.12 CA.27: 3 residues within 4Å: Chain C: E.4 Ligands: HEC.21, CA.26 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.4

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

CL.8: 8 residues within 4Å: Chain A: I.59, R.62 Chain B: I.59, R.62 Chain C: I.59, R.62 Ligands: CL.18, CL.28 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.41 Chain B: K.41 Chain C: K.41 Ligands: CL.19, CL.29 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.34, H.73, A.76 Ligand excluded by PLIP CL.18: 8 residues within 4Å: Chain A: I.59, R.62 Chain B: I.59, R.62 Chain C: I.59, R.62 Ligands: CL.8, CL.28 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: K.41 Chain B: K.41 Chain C: K.41 Ligands: CL.9, CL.29 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.34, H.73, A.76 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain A: I.59, R.62 Chain B: I.59, R.62 Chain C: I.59, R.62 Ligands: CL.8, CL.18 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain A: K.41 Chain B: K.41 Chain C: K.41 Ligands: CL.9, CL.19 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: R.34, H.73, A.76 Ligand excluded by PLIP

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
A

C
A

Soluble cytochrome b562

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