SMTL ID : 6ai5.1

Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 19 residues within 4Å: Chain A: E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, L.94, T.97, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:P.45, 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:R.106 Metal complexes: A:H.102 HEM.9: 19 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, 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 B, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:N.11, B:P.45, B:F.65, B:F.65, B:L.68, B:L.94, B:R.106 Hydrogen bonds: B:E.8 pi-Stacking: B:H.102 pi-Cation interactions: B:H.102, B:R.106 Metal complexes: B:H.102 HEM.14: 19 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, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.3, C:M.7, C:N.11, C:P.45, C:F.61, C:F.65, C:F.65, C:L.68, C:R.106 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 HEM.19: 17 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, N.11, L.14, M.33, P.45, P.46, F.61, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:R.106 Hydrogen bonds: D:L.3, D:E.8 Water bridges: D:E.4 pi-Stacking: D:H.102, D:H.102 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: H.73, H.77 Chain B: H.63 Chain C: D.74 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:H.73, A:H.77, C:D.74, C:D.74, B:H.63 ZN.3: 4 residues within 4Å: Chain A: E.86, H.89 Chain D: H.100 Ligands: CL.4 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:H.100, A:E.86, A:E.86, A:H.89 ZN.6: 4 residues within 4Å: Chain A: H.63 Chain B: H.73, H.77 Chain D: D.74 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 1 interactions with chain A Metal complexes: D:D.74, B:H.73, B:H.77, A:H.63 ZN.7: 4 residues within 4Å: Chain A: D.74 Chain C: H.73, H.77 Chain D: H.63 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Metal complexes: C:H.73, C:H.77, A:D.74, A:D.74, D:H.63 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.18 ZN.10: 2 residues within 4Å: Chain B: H.89 Chain C: H.100 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.89, C:H.100, H2O.11 ZN.12: 3 residues within 4Å: Chain B: H.100 Chain C: E.86, H.89 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.100, C:E.86, C:E.86, C:H.89, H2O.13 ZN.13: 4 residues within 4Å: Chain B: D.74 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 B Metal complexes: C:H.63, D:H.73, D:H.77, B:D.74

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: E.86, H.89 Chain D: H.100, A.104 Ligands: ZN.3 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: E.86, H.89 Chain C: H.100 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: H.77 Chain B: H.63 Chain C: L.78, E.81 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: W.41, S.42, A.43, M.58, R.62 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain D: A.24, D.28 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.8, D.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:D.12, A:D.12 MG.11: 3 residues within 4Å: Chain B: T.9, N.13, K.32 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: D.2, D.5 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.2, H2O.11 MG.21: 5 residues within 4Å: Chain B: H.77, N.80 Chain D: L.78, E.81, K.83 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, H2O.2, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, W.J. et al., Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3. To Be Published

Release Date

2019-09-11

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Soluble cytochrome b562