SMTL ID : 5awi.1

Domain-swapped cytochrome cb562 dimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 17 residues within 4Å: Chain A: F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 Chain B: L.3, E.4, M.7, E.8, L.10, N.11, M.33, P.45, P.46 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:N.11, B:P.45, A:F.65, A:F.65, A:F.65, A:R.106 Hydrogen bonds: B:E.8 Water bridges: B:E.4 pi-Stacking: A:H.102, A:H.102, A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.8: 15 residues within 4Å: Chain A: E.4, M.7, E.8, N.11, M.33, P.45, P.46 Chain B: F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:F.61, B:F.65, B:F.65, B:F.65, B:R.106, A:M.7, A:N.11, A:P.45 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 Hydrogen bonds: A:E.8

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.5 Ligands: SO4.6, SO4.7, ZN.9, SO4.12 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.5, A:D.5 ZN.3: 3 residues within 4Å: Chain A: D.5, E.8 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.8, A:E.8 ZN.4: 2 residues within 4Å: Chain A: D.2 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.2 ZN.5: 2 residues within 4Å: Chain A: A.1, D.39 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:D.39 ZN.9: 5 residues within 4Å: Chain B: D.5 Ligands: ZN.2, SO4.7, ZN.10, SO4.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.5 ZN.10: 3 residues within 4Å: Chain B: E.4, D.5 Ligands: ZN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.4, B:E.4, B:D.5, H2O.2 ZN.11: 2 residues within 4Å: Chain B: A.1, D.39 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.1, B:D.39, H2O.2

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 6 residues within 4Å: Chain A: D.5, E.8 Ligands: ZN.2, ZN.3, SO4.7, SO4.12 No protein-ligand interaction detected (PLIP) SO4.7: 10 residues within 4Å: Chain A: D.2, D.5 Chain B: A.1, D.2, D.5 Ligands: ZN.2, ZN.4, SO4.6, ZN.9, SO4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2 Water bridges: B:D.2 SO4.12: 5 residues within 4Å: Chain B: D.5 Ligands: ZN.2, SO4.6, SO4.7, ZN.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyamoto, T. et al., Domain-swapped cytochrome cb562 dimer and its nanocage encapsulating a Zn-SO4 cluster in the internal cavity. Chem Sci (2015)

Release Date

2015-10-21

Peptides

Soluble cytochrome b562: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Soluble cytochrome b562