SMTL ID : 6gmi.1

Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in E. coli's Periplasm.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x 4IR: {N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(chloro)[(1,2,3,4,5-eta)-1,2,3,4,5-pentamethylcyclopentadienyl]iridium(III)(Non-covalent)

4IR.1: 24 residues within 4Å: Chain A: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, S.87, T.89, W.91, W.107, L.109, V.111, T.114, A.143, L.146, D.150 Chain C: W.142, L.146 Ligands: 4IR.11 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.49, A:W.78, A:W.78, A:W.78, A:V.111, A:V.111, A:A.143 Hydrogen bonds: A:N.22, A:S.26, A:Y.42, A:S.44, A:N.48, A:S.87, A:S.87, A:D.150 4IR.6: 24 residues within 4Å: Chain B: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, S.87, T.89, W.91, W.107, L.109, V.111, T.114, A.143, L.146, D.150 Chain D: W.142, L.146 Ligands: 4IR.16 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.49, B:W.78, B:W.78, B:W.78, B:V.111, B:V.111, B:A.143 Hydrogen bonds: B:N.22, B:S.26, B:S.44, B:N.48, B:S.87, B:S.87, B:D.150 4IR.11: 24 residues within 4Å: Chain A: W.142, L.146 Chain C: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, S.87, T.89, W.91, W.107, L.109, V.111, T.114, A.143, L.146, D.150 Ligands: 4IR.1 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.49, C:W.78, C:W.78, C:W.78, C:V.111, C:V.111, C:A.143 Hydrogen bonds: C:N.22, C:S.26, C:Y.42, C:S.44, C:N.48, C:S.87, C:S.87, C:D.150 4IR.16: 24 residues within 4Å: Chain B: W.142, L.146 Chain D: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, S.87, T.89, W.91, W.107, L.109, V.111, T.114, A.143, L.146, D.150 Ligands: 4IR.6 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.49, D:W.78, D:W.78, D:W.78, D:V.111, D:V.111, D:A.143 Hydrogen bonds: D:N.22, D:S.26, D:S.44, D:N.48, D:S.87, D:S.87, D:D.150

16 x IR3: IRIDIUM (III) ION(Non-covalent)

IR3.2: 1 residues within 4Å: Chain A: H.86 Ligand excluded by PLIP IR3.3: 2 residues within 4Å: Chain A: H.149 Ligands: IR3.5 Ligand excluded by PLIP IR3.4: 3 residues within 4Å: Chain A: H.149 Ligands: IR3.5, IR3.9 Ligand excluded by PLIP IR3.5: 3 residues within 4Å: Chain A: H.149 Ligands: IR3.3, IR3.4 Ligand excluded by PLIP IR3.7: 1 residues within 4Å: Chain B: H.86 Ligand excluded by PLIP IR3.8: 2 residues within 4Å: Chain B: H.149 Ligands: IR3.10 Ligand excluded by PLIP IR3.9: 3 residues within 4Å: Chain B: H.149 Ligands: IR3.4, IR3.10 Ligand excluded by PLIP IR3.10: 3 residues within 4Å: Chain B: H.149 Ligands: IR3.8, IR3.9 Ligand excluded by PLIP IR3.12: 1 residues within 4Å: Chain C: H.86 Ligand excluded by PLIP IR3.13: 2 residues within 4Å: Chain C: H.149 Ligands: IR3.15 Ligand excluded by PLIP IR3.14: 3 residues within 4Å: Chain C: H.149 Ligands: IR3.15, IR3.19 Ligand excluded by PLIP IR3.15: 3 residues within 4Å: Chain C: H.149 Ligands: IR3.13, IR3.14 Ligand excluded by PLIP IR3.17: 1 residues within 4Å: Chain D: H.86 Ligand excluded by PLIP IR3.18: 2 residues within 4Å: Chain D: H.149 Ligands: IR3.20 Ligand excluded by PLIP IR3.19: 3 residues within 4Å: Chain D: H.149 Ligands: IR3.14, IR3.20 Ligand excluded by PLIP IR3.20: 3 residues within 4Å: Chain D: H.149 Ligands: IR3.18, IR3.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in Escherichia coli's Periplasm. J. Am. Chem. Soc. (2018)

Release Date

2018-10-10

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin