SMTL ID : 6s50.1

scdSav(SARK)mv2 - Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

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: 21 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, A.121, L.124, D.128 Chain B: W.304 Ligands: 4IR.8 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:W.304, A:W.79, A:W.79, A:W.79, A:L.110 Hydrogen bonds: A:N.23, A:S.27, A:S.45, A:N.49, A:S.88, A:S.88, A:S.112, A:A.121, A:D.128 4IR.2: 19 residues within 4Å: Chain A: L.209, D.211, Y.227, T.229, R.231, G.232, N.233, W.263, A.270, S.272, T.274, W.276, W.292, L.294, R.296, K.305 Chain B: W.120, L.124 Ligands: 4IR.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.263, A:W.263, A:W.263, A:R.296, A:K.305 Hydrogen bonds: A:Y.227, A:T.229, A:N.233, A:S.272, A:S.272, A:K.305 4IR.7: 22 residues within 4Å: Chain A: W.304, L.308 Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, A.121, D.128 Ligands: 4IR.2 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:T.114, B:A.121 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:N.49, B:S.88, B:S.88, B:S.112, B:D.128 4IR.8: 17 residues within 4Å: Chain A: W.120 Chain B: D.211, Y.227, T.229, R.231, G.232, N.233, W.263, A.270, S.272, T.274, W.276, W.292, L.294, R.296, K.305 Ligands: 4IR.1 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.263, B:W.263, B:W.263, B:L.294, B:K.305 Hydrogen bonds: B:T.229, B:N.233, B:S.272, B:S.272

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.81, N.82, Y.83, R.84, N.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.85 GOL.4: 4 residues within 4Å: Chain A: H.127, T.129 Chain B: Q.24, H.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.24, A:T.129 Water bridges: B:H.127, B:H.127 GOL.5: 7 residues within 4Å: Chain A: V.55, K.80, N.81, N.82, D.220, R.243, S.246 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.80, A:K.80, A:K.80, A:D.220, A:R.243, A:S.246 GOL.9: 5 residues within 4Å: Chain B: N.81, N.82, Y.83, R.84, N.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.84 Water bridges: B:K.80, B:K.80 GOL.10: 5 residues within 4Å: Chain B: K.264, N.265, Y.267, R.268, N.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.267, B:N.269 GOL.11: 3 residues within 4Å: Chain B: V.228, T.229, A.230 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.210, B:V.228

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 1 residues within 4Å: Chain A: A.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., Breaking Symmetry: Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes. J.Am.Chem.Soc. (2019)

Release Date

2019-09-25

Peptides

Streptavidin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Streptavidin