SMTL ID : 6x8x.1

Cu-bound structure of an engineered metal-dependent protein trimer, TriCyt1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: E.4, M.7, E.8, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, K.95, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:L.14, A:P.45, A:F.65, A:F.65, A:L.68 Hydrogen bonds: A:E.4, A:R.106 Salt bridges: A:R.106 Metal complexes: A:H.102 HEC.8: 19 residues within 4Å: Chain B: E.4, M.7, E.8, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, K.95, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.11 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:N.11, B:L.14, B:P.45, B:F.65, B:F.65, B:L.68 Hydrogen bonds: B:E.4, B:R.106 Salt bridges: B:R.106 Metal complexes: B:H.102 HEC.15: 19 residues within 4Å: Chain C: E.4, M.7, E.8, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, K.95, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.18 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:N.11, C:L.14, C:P.45, C:F.65, C:F.65, C:L.68 Hydrogen bonds: C:E.4, C:R.106 Salt bridges: C:R.106 Metal complexes: C:H.102

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

CU.2: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: CU.9, CU.16 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 CU.9: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: CU.2, CU.16 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 CU.16: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: CU.2, CU.9 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

15 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 3 residues within 4Å: Chain A: K.19, D.21 Ligands: CA.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.19, A:D.21, H2O.1 CA.4: 3 residues within 4Å: Chain A: E.4, E.8 Ligands: HEC.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, H2O.1 CA.5: 1 residues within 4Å: Chain A: E.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.8, A:E.8 CA.6: 4 residues within 4Å: Chain A: K.19, A.20, D.21 Ligands: CA.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.19, A:D.21, H2O.1 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain B: K.19, D.21 Ligands: CA.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.19, B:D.21, H2O.2 CA.11: 3 residues within 4Å: Chain B: E.4, E.8 Ligands: HEC.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, H2O.1 CA.12: 1 residues within 4Å: Chain B: E.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.8, B:E.8 CA.13: 4 residues within 4Å: Chain B: K.19, A.20, D.21 Ligands: CA.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.19, B:D.21, H2O.2 CA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 3 residues within 4Å: Chain C: K.19, D.21 Ligands: CA.20 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.19, C:D.21, H2O.3 CA.18: 3 residues within 4Å: Chain C: E.4, E.8 Ligands: HEC.15 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, H2O.2 CA.19: 1 residues within 4Å: Chain C: E.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.8, C:E.8 CA.20: 4 residues within 4Å: Chain C: K.19, A.20, D.21 Ligands: CA.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.19, C:D.21, H2O.3 CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (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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