SMTL ID : 8by0.1

streptavidin mutant S112I K121R with an iridium catalyst for CH activation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NOF: tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate(Non-covalent)

NOF.1: 26 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, H.86, S.87, T.89, W.91, W.107, L.109, I.111, G.112, R.120, L.123, D.127 Chain C: W.119, R.120, L.123 Ligands: NOF.7 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:W.78, A:W.78, A:W.78, A:A.85, A:I.111, A:L.123, C:W.119, C:W.119, C:R.120 Hydrogen bonds: A:N.22, A:Y.42, A:S.44, A:S.44, A:N.48, A:S.87, A:D.127 NOF.4: 26 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, H.86, S.87, T.89, W.91, W.107, L.109, I.111, G.112, R.120, L.123, D.127 Chain D: W.119, R.120, L.123 Ligands: NOF.10 16 PLIP interactions: 3 interactions with chain D, 13 interactions with chain B, Hydrophobic interactions: D:W.119, D:W.119, D:R.120, B:W.78, B:W.78, B:W.78, B:A.85, B:I.111, B:L.123 Hydrogen bonds: B:N.22, B:Y.42, B:S.44, B:S.44, B:N.48, B:S.87, B:D.127 NOF.7: 26 residues within 4Å: Chain A: W.119, R.120, L.123 Chain C: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, H.86, S.87, T.89, W.91, W.107, L.109, I.111, G.112, R.120, L.123, D.127 Ligands: NOF.1 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A, Hydrophobic interactions: C:W.78, C:W.78, C:W.78, C:A.85, C:I.111, C:L.123, A:W.119, A:W.119, A:R.120 Hydrogen bonds: C:N.22, C:Y.42, C:S.44, C:S.44, C:N.48, C:S.87, C:D.127 NOF.10: 26 residues within 4Å: Chain B: W.119, R.120, L.123 Chain D: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, A.49, W.78, A.85, H.86, S.87, T.89, W.91, W.107, L.109, I.111, G.112, R.120, L.123, D.127 Ligands: NOF.4 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain B, Hydrophobic interactions: D:W.78, D:W.78, D:W.78, D:A.85, D:I.111, D:L.123, B:W.119, B:W.119, B:R.120 Hydrogen bonds: D:N.22, D:Y.42, D:S.44, D:S.44, D:N.48, D:S.87, D:D.127

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

SO4.2: 4 residues within 4Å: Chain A: V.46, G.47 Chain C: W.119, R.120 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.47, C:W.119 Salt bridges: C:R.120 SO4.3: 2 residues within 4Å: Chain A: N.48, R.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.83 SO4.5: 4 residues within 4Å: Chain B: V.46, G.47 Chain D: W.119, R.120 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:W.119, B:G.47 Salt bridges: D:R.120 SO4.6: 2 residues within 4Å: Chain B: N.48, R.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.83 SO4.8: 4 residues within 4Å: Chain A: W.119, R.120 Chain C: V.46, G.47 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.119, C:G.47 Salt bridges: A:R.120 SO4.9: 2 residues within 4Å: Chain C: N.48, R.83 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.83 SO4.11: 4 residues within 4Å: Chain B: W.119, R.120 Chain D: V.46, G.47 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:W.119, D:G.47 Salt bridges: B:R.120 SO4.12: 2 residues within 4Å: Chain D: N.48, R.83 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igareta, N.V. et al., streptavidin mutant S112I with an iridium catalyst for CH activation. To Be Published

Release Date

2023-12-20

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin