SMTL ID : 4u9e.1

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 10 residues within 4Å: Chain A: E.4, M.7, N.11, F.61, F.65, C.98, C.101, H.102, R.106 Ligands: CA.4 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:F.65 pi-Stacking: A:H.102, A:H.102, A:H.102, A:H.102 Metal complexes: A:H.102 HEC.9: 10 residues within 4Å: Chain B: E.4, M.7, N.11, F.61, F.65, C.98, C.101, H.102, R.106 Ligands: CA.12 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:M.7, B:N.11, B:F.65 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102, B:H.102, B:H.102, B:H.102 Metal complexes: B:H.102 HEC.17: 10 residues within 4Å: Chain C: E.4, M.7, N.11, F.61, F.65, C.98, C.101, H.102, R.106 Ligands: CA.20 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:M.7, C:N.11, C:F.65 Hydrogen bonds: C:E.4 pi-Stacking: C:H.102, C:H.102, C:H.102, C:H.102 Metal complexes: C:H.102 HEC.25: 10 residues within 4Å: Chain D: E.4, M.7, N.11, F.61, F.65, C.98, C.101, H.102, R.106 Ligands: CA.28 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:M.7, D:N.11, D:F.65 pi-Stacking: D:H.102, D:H.102, D:H.102, D:H.102 Metal complexes: D:H.102

20 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 4 residues within 4Å: Chain A: D.5, E.8 Ligands: CA.4, CA.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.5, A:E.8, A:E.8 CA.3: 2 residues within 4Å: Chain A: K.19, D.21 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.19, A:D.21, H2O.1 CA.4: 4 residues within 4Å: Chain A: E.4, E.8 Ligands: HEC.1, CA.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.4, A:E.8, H2O.1 CA.5: 1 residues within 4Å: Ligands: CA.21 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.8 Ligands: CA.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, H2O.1 CA.10: 4 residues within 4Å: Chain B: D.5, E.8 Ligands: CA.12, CA.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.5, B:E.8, B:E.8 CA.11: 2 residues within 4Å: Chain B: K.19, D.21 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.19, B:D.21, H2O.5 CA.12: 4 residues within 4Å: Chain B: E.4, E.8 Ligands: HEC.9, CA.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.4, B:E.8, H2O.5 CA.13: 1 residues within 4Å: Ligands: CA.29 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain B: E.8 Ligands: CA.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, H2O.4 CA.18: 4 residues within 4Å: Chain C: D.5, E.8 Ligands: CA.20, CA.22 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.5, C:E.8, C:E.8 CA.19: 2 residues within 4Å: Chain C: K.19, D.21 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.19, C:D.21, H2O.8 CA.20: 4 residues within 4Å: Chain C: E.4, E.8 Ligands: HEC.17, CA.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.4, C:E.8, H2O.8 CA.21: 1 residues within 4Å: Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.22: 2 residues within 4Å: Chain C: E.8 Ligands: CA.18 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, H2O.8 CA.26: 4 residues within 4Å: Chain D: D.5, E.8 Ligands: CA.28, CA.30 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.5, D:E.8, D:E.8 CA.27: 2 residues within 4Å: Chain D: K.19, D.21 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.19, D:D.21, H2O.11 CA.28: 4 residues within 4Å: Chain D: E.4, E.8 Ligands: HEC.25, CA.26 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.4, D:E.8, H2O.11 CA.29: 1 residues within 4Å: Ligands: CA.13 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain D: E.8 Ligands: CA.26 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, H2O.11

8 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.63 Chain C: H.73, H.77 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.63, C:H.73, C:H.77, H2O.1 ZN.8: 3 residues within 4Å: Chain A: H.100 Chain D: E.86, H.89 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.86, D:E.86, D:H.89, A:H.100, H2O.11 ZN.15: 3 residues within 4Å: Chain B: H.63 Chain D: H.73, H.77 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.73, D:H.77, B:H.63, H2O.4 ZN.16: 3 residues within 4Å: Chain B: H.100 Chain C: E.86, H.89 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.86, C:E.86, C:H.89, B:H.100, H2O.8 ZN.23: 3 residues within 4Å: Chain A: H.73, H.77 Chain C: H.63 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.73, A:H.77, C:H.63, H2O.8 ZN.24: 3 residues within 4Å: Chain B: E.86, H.89 Chain C: H.100 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.86, B:E.86, B:H.89, C:H.100, H2O.5 ZN.31: 3 residues within 4Å: Chain B: H.73, H.77 Chain D: H.63 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.73, B:H.77, D:H.63, H2O.11 ZN.32: 3 residues within 4Å: Chain A: E.86, H.89 Chain D: H.100 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.86, A:E.86, A:H.89, D:H.100, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, W.J. et al., A designed supramolecular protein assembly with in vivo enzymatic activity. Science (2014)

Release Date

2015-01-21

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Soluble cytochrome b562