SMTL ID : 7rwu.1

Crystal structure of Ni-bound RIDC1 variant in the presence of reductant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

NI.1: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.7, NI.13 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.2: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.8, NI.14 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 NI.3: 3 residues within 4Å: Chain A: A.1, D.39 Ligands: TRS.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:D.39 NI.7: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.1, NI.13 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.8: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.2, NI.14 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 NI.9: 3 residues within 4Å: Chain B: A.1, D.39 Ligands: TRS.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.1, B:D.39 NI.13: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.1, NI.7 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.14: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.2, NI.8 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 NI.15: 3 residues within 4Å: Chain C: A.1, D.39 Ligands: TRS.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.1, C:D.39

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 5 residues within 4Å: Chain A: A.1, N.6, D.39, S.42 Ligands: NI.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.1, A:D.39, A:S.42, A:S.42 Water bridges: A:N.6 TRS.10: 5 residues within 4Å: Chain B: A.1, N.6, D.39, S.42 Ligands: NI.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.1, B:D.39, B:S.42, B:S.42 Water bridges: B:N.6 TRS.16: 5 residues within 4Å: Chain C: A.1, N.6, D.39, S.42 Ligands: NI.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.1, C:D.39, C:D.39, C:S.42, C:S.42 Water bridges: C:N.6

3 x HEC: HEME C(Non-covalent)

HEC.5: 20 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, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 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:L.68, A:L.68, A:R.106, A:R.106 Hydrogen bonds: A:E.8 Water bridges: A:E.4, A:E.4 Metal complexes: A:H.102 HEC.11: 20 residues within 4Å: Chain B: 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, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 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:L.68, B:L.68, B:R.106, B:R.106 Water bridges: B:E.4, B:E.4 Metal complexes: B:H.102 HEC.17: 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, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 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:L.68, C:L.68, C:R.106, C:R.106 Water bridges: C:E.4, C:E.4, C:R.106 Metal complexes: C:H.102

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

CL.6: 2 residues within 4Å: Chain A: D.2, L.3 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: D.2, L.3 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: D.2, L.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakkis, A. et al., Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Chem.Commun.(Camb.) (2022)

Release Date

2022-06-29

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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