SMTL ID : 6wza.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, N.11, L.14, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, R.106 Ligands: MPD.6, MPD.7 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.3, A:E.4, A:M.7, A:N.11, A:L.14, A:P.45, A:F.65, A:F.65, A:F.65, A:T.97, A:R.106 Hydrogen bonds: A:E.4 Metal complexes: A:H.102 HEC.8: 18 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 Ligands: MPD.12 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Water bridges: B:E.4, B:R.106 Metal complexes: B:H.102 HEC.13: 18 residues within 4Å: Chain C: L.3, E.4, M.7, E.8, N.11, P.45, P.46, F.61, G.64, F.65, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 Ligands: NA.14 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:E.4, C:M.7, C:N.11, C:P.45, C:F.65, C:F.65, C:F.65, C:L.94, C:R.106, C:R.106 Hydrogen bonds: C:E.4, C:E.8 Metal complexes: C:H.102

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

NI.2: 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 A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.73, A:H.77, B:H.73, B:H.77, C:H.73, C:H.77

5 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: Q.41, K.42, A.43, R.62 No protein-ligand interaction detected (PLIP) NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.14: 3 residues within 4Å: Chain C: E.4, E.8 Ligands: HEC.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.4, C:E.8 NA.15: 2 residues within 4Å: Chain C: D.2, D.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.5 NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain A: R.34 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: H.59 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Q.41, M.58, R.62 Chain C: H.59 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: H.77 Chain C: H.73 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: H.59, R.62 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: R.34 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain A: H.102, R.106 Ligands: HEC.1, MPD.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.106 MPD.7: 8 residues within 4Å: Chain A: N.11, L.14, K.95, C.98, N.99, H.102 Ligands: HEC.1, MPD.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.14, A:K.95 Hydrogen bonds: A:N.11 MPD.12: 6 residues within 4Å: Chain B: N.11, K.95, C.98, N.99, H.102 Ligands: HEC.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.11, B:N.99

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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