SMTL ID : 3c62.1

Tetrameric Cytochrome cb562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized by Interprotein Zinc Coordination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: H.63 Chain D: H.59 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Metal complexes: B:H.63, A:H.73, A:H.77, D:H.59 ZN.4: 4 residues within 4Å: Chain A: H.63 Chain B: H.73, H.77 Chain C: H.59 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.73, B:H.77, A:H.63, C:H.59 ZN.9: 4 residues within 4Å: Chain B: H.59 Chain C: H.73, H.77 Chain D: H.63 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: C:H.73, C:H.77, B:H.59, D:H.63 ZN.11: 4 residues within 4Å: Chain A: H.59 Chain C: H.63 Chain D: H.73, H.77 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Metal complexes: C:H.63, D:H.73, D:H.77, A:H.59

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.4 Ligands: HEM.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.4, H2O.2 CA.5: 1 residues within 4Å: Chain B: D.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.12, H2O.9 CA.6: 2 residues within 4Å: Chain B: D.2, E.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.2, B:D.2, B:E.4 CA.7: 1 residues within 4Å: Chain B: D.28 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.28, H2O.6 CA.12: 2 residues within 4Å: Chain D: D.5, E.8 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.5, D:E.8, H2O.17, H2O.19, H2O.20

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 19 residues within 4Å: Chain A: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, L.94, C.98, C.101, H.102, Y.105, R.106 Ligands: CA.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:L.10, A:L.10, A:P.45, A:F.65, A:F.65, A:F.65, A:L.68, A:L.94, A:R.106 pi-Stacking: A:H.102, A:H.102 pi-Cation interactions: A:H.102 Metal complexes: A:H.102 HEM.8: 19 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, G.64, F.65, L.68, L.94, C.98, C.101, H.102, Y.105, R.106 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.10, B:L.14, B:P.45, B:F.65, B:F.65, B:F.65, B:L.68, B:L.68, B:L.94, B:R.106 Water bridges: B:R.106, B:R.106 pi-Stacking: B:H.102 Metal complexes: B:H.102 HEM.10: 17 residues within 4Å: Chain C: L.3, E.4, M.7, N.11, L.14, P.45, P.46, F.61, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:P.45, C:F.61, C:F.65, C:L.68, C:L.94, C:R.106 Hydrogen bonds: C:E.4 pi-Stacking: C:H.102, C:H.102 pi-Cation interactions: C:H.102, C:H.102, C:R.106 Metal complexes: C:H.102 HEM.13: 18 residues within 4Å: Chain D: L.3, E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, L.94, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:E.4, D:M.7, D:L.10, D:L.14, D:P.45, D:F.61, D:F.65, D:L.68, D:L.68, D:L.94, D:R.106, D:R.106 Salt bridges: D:R.106 pi-Stacking: D:H.102, D:H.102, D:H.102 Metal complexes: D:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado, E.N. et al., Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation. J.Am.Chem.Soc. (2008)

Release Date

2008-05-06

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562