SMTL ID : 6wz1.1

Mn-bound structure of an engineered protein trimer, TriCyt3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 21 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, F.65, C.98, C.101, H.102, Y.105, R.106 Chain B: E.8, D.12, V.16 Ligands: CA.2 18 PLIP interactions: 5 interactions with chain B, 13 interactions with chain A, Hydrophobic interactions: B:V.16, 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:R.106 Hydrogen bonds: B:E.8 Water bridges: B:D.12, B:K.19, B:K.19, A:E.4 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.5: 20 residues within 4Å: Chain B: L.3, E.4, M.7, N.11, L.14, M.33, P.45, F.61, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 Chain C: N.11, K.15, R.106 Ligands: HEC.10, CL.11 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:L.3, B:M.7, B:N.11, B:L.14, B:P.45, B:F.65, B:F.65, B:F.65 Hydrogen bonds: B:E.4, C:N.11 Salt bridges: B:R.106, C:K.15, C:K.15 Metal complexes: B:H.102 Water bridges: C:K.15, C:K.15 HEC.10: 22 residues within 4Å: Chain B: N.11, D.12, R.106 Chain C: L.3, E.4, M.7, N.11, 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 Ligands: CA.3, HEC.5 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:R.106 Hydrogen bonds: C:E.4 Water bridges: C:E.4 pi-Cation interactions: C:R.106 Metal complexes: C:H.102

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.4 Chain B: E.8, D.12 Ligands: HEC.1, CA.3 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.12, A:E.4, H2O.2, H2O.8 CA.3: 6 residues within 4Å: Chain A: E.4 Chain B: D.12 Chain C: E.4 Ligands: CA.2, CA.4, HEC.10 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.12, A:E.4, A:E.4, C:E.4, H2O.5 CA.4: 3 residues within 4Å: Chain A: E.4 Chain C: E.4 Ligands: CA.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:E.4, C:E.4, H2O.1, H2O.1, H2O.7 CA.12: 3 residues within 4Å: Chain A: D.2 Chain C: D.2, D.5 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.2, C:D.5, A:D.2, H2O.1, H2O.2

1 x MN: MANGANESE (II) ION(Non-covalent)

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

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

CL.7: 3 residues within 4Å: Chain B: R.34, H.73, A.76 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: R.62 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: K.41 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: N.11, K.15, K.95 Chain C: R.106 Ligands: HEC.5 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
B

B
A

C
C

Soluble cytochrome b562

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