SMTL ID : 4u9d.1

Crystal Structure of the Zn-directed tetramer of the engineered cyt cb562 variant, AB3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 15 residues within 4Å: Chain A: M.7, L.10, N.11, L.14, P.45, P.46, F.61, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:N.11, A:P.45, A:F.61, A:F.65, A:F.65, A:L.68, A:T.97 Salt bridges: A:R.106 pi-Stacking: A:H.102, A:H.102 pi-Cation interactions: A:H.102, A:R.106, A:R.106 Metal complexes: A:H.102 HEC.7: 15 residues within 4Å: Chain B: E.4, M.7, L.10, N.11, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.10, B:N.11, B:P.45, B:F.65, B:F.65, B:L.68, B:R.106 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102, B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.11: 16 residues within 4Å: Chain C: 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, R.106 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:M.7, C:N.11, C:L.14, C:P.45, C:F.65, C:F.65, C:L.68 Hydrogen bonds: C:E.4 pi-Stacking: C:H.102, C:H.102, C:H.102, C:H.102 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.12: 14 residues within 4Å: Chain D: L.3, E.4, M.7, L.10, N.11, P.45, F.61, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:L.10, D:P.45, D:F.61, D:F.65, D:L.68, D:Y.105 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: E.86, H.89 Chain C: H.100, K.104 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.86, A:E.86, A:H.89, C:H.100 ZN.3: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: D.74 Chain D: H.63 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 2 interactions with chain B Metal complexes: D:H.63, A:H.73, A:H.77, B:D.74, B:D.74 ZN.4: 4 residues within 4Å: Chain A: D.74 Chain B: H.73, H.77 Chain C: H.63 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Metal complexes: B:H.73, B:H.77, A:D.74, A:D.74, C:H.63 ZN.5: 4 residues within 4Å: Chain A: H.100, K.104 Chain C: E.86, H.89 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Metal complexes: A:H.100, C:E.86, C:E.86, C:H.89 ZN.6: 4 residues within 4Å: Chain A: H.63 Chain C: D.74 Chain D: H.73, H.77 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 interactions with chain A Metal complexes: D:H.73, D:H.77, C:D.74, C:D.74, A:H.63 ZN.8: 4 residues within 4Å: Chain B: E.86, H.89 Chain D: H.100, K.104 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Metal complexes: B:E.86, B:E.86, B:H.89, D:H.100 ZN.9: 4 residues within 4Å: Chain B: H.63 Chain C: H.73, H.77 Chain D: D.74 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Metal complexes: C:H.73, C:H.77, B:H.63, D:D.74, D:D.74 ZN.10: 4 residues within 4Å: Chain B: H.100, K.104 Chain D: E.86, H.89 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.86, D:H.89, B:H.100

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

2015-01-14

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562