SMTL ID : 8by1.1

streptavidin with an iridium catalyst for CH activation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 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: 29 residues within 4Å: Chain A: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, H.76, S.77, T.79, W.81, W.97, L.99, S.101, G.102, T.103, K.110, S.111, T.112, L.113, D.117 Chain C: W.109, K.110, L.113 Ligands: NOF.7 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.68, A:W.68, A:W.68, A:H.76, A:L.113, A:L.113, C:W.109, C:W.109 Hydrogen bonds: A:N.12, A:Y.32, A:S.34, A:S.34, A:N.38, A:S.77, A:D.117 NOF.4: 29 residues within 4Å: Chain B: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, H.76, S.77, T.79, W.81, W.97, L.99, S.101, G.102, T.103, K.110, S.111, T.112, L.113, D.117 Chain D: W.109, K.110, L.113 Ligands: NOF.10 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain D, Hydrophobic interactions: B:W.68, B:W.68, B:W.68, B:H.76, B:L.113, B:L.113, D:W.109, D:W.109 Hydrogen bonds: B:N.12, B:Y.32, B:S.34, B:S.34, B:N.38, B:S.77, B:D.117 NOF.7: 29 residues within 4Å: Chain A: W.109, K.110, L.113 Chain C: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, H.76, S.77, T.79, W.81, W.97, L.99, S.101, G.102, T.103, K.110, S.111, T.112, L.113, D.117 Ligands: NOF.1 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:W.68, C:W.68, C:W.68, C:H.76, C:L.113, C:L.113, A:W.109, A:W.109 Hydrogen bonds: C:N.12, C:Y.32, C:S.34, C:S.34, C:N.38, C:S.77, C:D.117 NOF.10: 29 residues within 4Å: Chain B: W.109, K.110, L.113 Chain D: N.12, L.14, S.16, Y.32, S.34, V.36, G.37, N.38, A.39, W.68, A.75, H.76, S.77, T.79, W.81, W.97, L.99, S.101, G.102, T.103, K.110, S.111, T.112, L.113, D.117 Ligands: NOF.4 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: D:W.68, D:W.68, D:W.68, D:H.76, D:L.113, D:L.113, B:W.109, B:W.109 Hydrogen bonds: D:N.12, D:Y.32, D:S.34, D:S.34, D:N.38, D:S.77, D:D.117

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

SO4.2: 3 residues within 4Å: Chain A: G.37, A.39, R.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.73 SO4.3: 4 residues within 4Å: Chain A: W.109, K.110 Chain C: V.36, G.37 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:W.109, A:W.109 Salt bridges: A:K.110 Hydrogen bonds: C:G.37 SO4.5: 3 residues within 4Å: Chain B: G.37, A.39, R.73 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.73 SO4.6: 4 residues within 4Å: Chain B: W.109, K.110 Chain D: V.36, G.37 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.37 Water bridges: B:W.109, B:W.109 Salt bridges: B:K.110 SO4.8: 3 residues within 4Å: Chain C: G.37, A.39, R.73 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.73 SO4.9: 4 residues within 4Å: Chain A: V.36, G.37 Chain C: W.109, K.110 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.37 Water bridges: C:W.109, C:W.109 Salt bridges: C:K.110 SO4.11: 3 residues within 4Å: Chain D: G.37, A.39, R.73 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.73 SO4.12: 4 residues within 4Å: Chain B: V.36, G.37 Chain D: W.109, K.110 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Water bridges: D:W.109, D:W.109 Salt bridges: D:K.110 Hydrogen bonds: B:G.37

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