SMTL ID : 5xzj.1

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, C96T/AB5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 12 residues within 4Å: Chain A: E.4, M.7, N.11, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:P.45, A:F.61, A:F.65, A:F.65, A:R.106 pi-Stacking: A:H.102, A:H.102, A:H.102 pi-Cation interactions: A:H.102, A:R.106 Metal complexes: A:H.102 HEC.7: 16 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, F.65, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:N.11, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102, B:H.102, B:H.102 Metal complexes: B:H.102 HEC.12: 13 residues within 4Å: Chain C: E.4, M.7, L.10, N.11, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:N.11, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:R.106 Hydrogen bonds: C:E.4 Water bridges: C:E.8, C:R.106, C:R.106 pi-Stacking: C:H.102, C:H.102 pi-Cation interactions: C:H.102 Metal complexes: C:H.102 HEC.16: 13 residues within 4Å: Chain D: E.4, M.7, N.11, M.33, P.45, P.46, F.61, F.65, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:M.7, D:N.11, D:P.45, D:F.61, D:F.65, D:F.65, D:F.65, D:R.106 pi-Stacking: D:H.102, D:H.102, D:H.102 Metal complexes: D:H.102

14 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain B: H.63 Chain C: D.74 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:H.73, A:H.77, C:D.74, B:H.63 ZN.3: 4 residues within 4Å: Chain A: E.89, H.93 Chain D: H.100 Ligands: CL.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:E.89, A:H.93, D:H.100 ZN.4: 2 residues within 4Å: Chain A: E.8, D.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:E.8, A:D.12 ZN.5: 1 residues within 4Å: Chain D: H.93 No protein-ligand interaction detected (PLIP) ZN.8: 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 A, 2 interactions with chain B, 1 interactions with chain D Metal complexes: A:H.63, B:H.73, B:H.77, D:D.74 ZN.9: 3 residues within 4Å: Chain B: E.89, H.93 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.89, B:E.89, B:H.93, C:H.100, H2O.6 ZN.10: 3 residues within 4Å: Chain B: E.81, K.83 Chain D: N.80 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.81, H2O.6, H2O.10, H2O.11 ZN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.13: 4 residues within 4Å: Chain A: D.74 Chain C: H.73, H.77 Chain D: H.63 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Metal complexes: C:H.73, C:H.77, D:H.63, A:D.74 ZN.14: 3 residues within 4Å: Chain B: H.100 Chain C: E.89, H.93 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.89, C:H.93, B:H.100 ZN.15: 2 residues within 4Å: Chain A: N.80 Chain C: E.81 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.81, H2O.1, H2O.3, H2O.9 ZN.17: 4 residues within 4Å: Chain B: D.74 Chain C: H.63 Chain D: H.73, H.77 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: D:H.73, D:H.77, C:H.63, B:D.74 ZN.18: 3 residues within 4Å: Chain A: H.100 Chain D: E.89, H.93 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.89, D:H.93, A:H.100, H2O.11 ZN.19: 1 residues within 4Å: Chain D: E.81 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.81, H2O.4, H2O.6, H2O.6, H2O.11

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

CL.6: 4 residues within 4Å: Chain A: E.89, H.93 Chain D: H.100 Ligands: ZN.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, W.J. et al., Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-beta-lactamases. J. Am. Chem. Soc. (2017)

Release Date

2017-12-20

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562