SMTL ID : 7rwy.2 (1 other biounit)

Crystal structure of a Fe-bound RIDC1 variant in the presence of reductant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 12 residues within 4Å: Chain A: I.69, G.70, H.73 Chain B: W.41, R.62, H.63, W.66 Chain C: A.38, I.69, G.70, H.73, A.74 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.41 Water bridges: A:H.73

3 x HEC: HEME C(Covalent)

HEC.2: 19 residues within 4Å: Chain A: L.3, 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 A, Hydrophobic interactions: A:L.3, A:M.7, A:L.10, A:L.10, A:N.11, A:P.45, A:F.65, A:F.65, A:F.65, A:L.68, A:L.68, A:R.106 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.5: 19 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, L.14, 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: TRS.6 11 PLIP interactions: 11 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:L.68, B:R.106 Hydrogen bonds: B:E.4 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.7: 21 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, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:N.11, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106 Hydrogen bonds: C:E.4 pi-Cation interactions: C:R.106 Metal complexes: C:H.102

2 x FE: FE (III) ION(Non-covalent)

FE.3: 5 residues within 4Å: Chain A: H.73 Chain B: H.59, H.63 Chain C: H.73, H.77 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.73, B:H.59, B:H.63 FE.4: 3 residues within 4Å: Chain A: H.59 Chain B: H.73, H.77 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.59, B:H.73, B:H.77, H2O.3, H2O.4

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

TRS.6: 6 residues within 4Å: Chain B: N.11, L.14, K.15, K.95, N.99 Ligands: HEC.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.95, B:K.95

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
B

B
C

C
F

Soluble cytochrome b562

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