SMTL ID : 5xzi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:L.3, A:E.4, A:M.7, A:L.10, A:L.10, A:L.14, A:F.61, A:F.65, A:F.65, A:F.65, A:T.97, A:R.106 Hydrogen bonds: A:E.4 Metal complexes: A:H.102 HEC.7: 18 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.3, B:E.4, B:M.7, B:L.10, B:L.10, B:L.14, B:F.61, B:F.65, B:F.65, B:F.65, B:T.97, B:R.106 Metal complexes: B:H.102 HEC.13: 18 residues within 4Å: Chain C: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.3, C:E.4, C:M.7, C:L.10, C:L.10, C:L.14, C:F.61, C:F.65, C:F.65, C:F.65, C:T.97, C:R.106 Metal complexes: C:H.102 HEC.19: 18 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.3, D:E.4, D:M.7, D:L.10, D:L.10, D:L.14, D:F.61, D:F.65, D:F.65, D:F.65, D:T.97, D:R.106 Hydrogen bonds: D:E.4 Metal complexes: D:H.102

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.63, W.66 Chain C: H.73, H.77 Ligands: CL.4 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.73, C:H.77, A:H.63 ZN.3: 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.2 ZN.8: 5 residues within 4Å: Chain B: H.63, W.66 Chain D: H.73, H.77 Ligands: CL.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Metal complexes: B:H.63, D:H.73, D:H.77 ZN.9: 3 residues within 4Å: Chain B: H.100 Chain C: E.89, H.93 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.100, C:E.89, C:H.93, H2O.5 ZN.14: 5 residues within 4Å: Chain A: H.73, H.77 Chain C: H.63, W.66 Ligands: CL.16 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.63, A:H.73, A:H.77 ZN.15: 3 residues within 4Å: Chain B: E.89, H.93 Chain C: H.100 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.89, B:H.93, C:H.100, H2O.7 ZN.20: 5 residues within 4Å: Chain B: H.73, H.77 Chain D: H.63, W.66 Ligands: CL.22 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.63, B:H.73, B:H.77 ZN.21: 3 residues within 4Å: Chain A: E.89, H.93 Chain D: H.100 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:H.100, A:E.89, A:H.93, H2O.10

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

CL.4: 6 residues within 4Å: Chain A: W.41, R.62, H.63 Chain C: H.73, H.77 Ligands: ZN.2 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: L.76 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: W.41, R.62, H.63 Chain D: H.73, H.77 Ligands: ZN.8 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: L.76 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain A: H.73, H.77 Chain C: W.41, R.62, H.63 Ligands: ZN.14 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: L.76 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain B: H.73, H.77 Chain D: W.41, R.62, H.63 Ligands: ZN.20 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: L.76 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
A

C
A

D
A

Soluble cytochrome b562