SMTL ID : 7tep.1

Crystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)(Non-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, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:L.14, A:F.61, A:F.65, A:R.106 Hydrogen bonds: A:E.4, A:E.4 pi-Cation interactions: A:R.106, A:R.106 Metal complexes: A:H.102 HEC.4: 19 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, 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 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:N.11, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:T.97, B:R.106 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102 Metal complexes: B:H.102 HEC.6: 22 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, R.62, G.64, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.3, C:L.10, C:N.11, C:P.45, C:F.65, C:F.65, C:F.65, C:L.68, C:L.94 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.8: 21 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, L.94, K.95, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:E.4, D:M.7, D:L.14, D:P.45, D:F.61, D:F.65, D:L.68, D:L.68, D:R.106, D:R.106 Hydrogen bonds: D:E.4 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

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

CU.2: 5 residues within 4Å: Chain A: H.77, E.81 Chain B: H.63 Chain C: Q.71, C.96 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.63, A:H.77, A:E.81, H2O.3 CU.3: 6 residues within 4Å: Chain A: Q.71, C.96, T.97 Chain C: H.77, E.81 Chain D: H.63 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Metal complexes: A:C.96, C:H.77, C:E.81, D:H.63 CU.5: 3 residues within 4Å: Chain B: H.77, E.81 Chain D: C.96 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.77, B:E.81, B:E.81, H2O.4 CU.7: 5 residues within 4Å: Chain B: C.96 Chain C: H.63, W.66 Chain D: H.77, E.81 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: D:H.77, D:E.81, C:H.63, B:C.96

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562

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