SMTL ID : 6y2t.1

Streptavidin wildtype with a biotC4-1 cofactor - an artificial iron hydroxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

8 x O6T: biotC4-1 cofactor(Non-covalent)

O6T.1: 27 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, N.118, K.121, S.122, L.124, D.128 Chain C: W.120, K.121, L.124 Ligands: O6T.9 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.79, A:W.79, A:L.110, A:T.114, A:L.124, C:W.120 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.88, A:S.88, A:S.112, A:D.128 O6T.3: 18 residues within 4Å: Chain A: T.114, T.115, E.116, A.119 Chain C: Q.24, H.127 Chain D: D.13, G.68, S.69, G.70, T.71, Q.95, Y.96, V.97, G.98, G.99, R.103, N.105 11 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: D:V.97, D:V.97, D:N.105, C:Q.24, A:E.116 Hydrogen bonds: D:D.13, D:G.70, D:Q.95, D:G.99, D:N.105, A:E.116 O6T.5: 27 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, N.118, K.121, S.122, L.124, D.128 Chain D: W.120, K.121, L.124 Ligands: O6T.13 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:W.79, B:W.79, B:L.110, B:T.114, B:L.124, D:W.120 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 O6T.7: 18 residues within 4Å: Chain B: T.114, T.115, E.116, A.119 Chain C: D.13, G.68, S.69, G.70, T.71, Q.95, Y.96, V.97, G.98, G.99, R.103, N.105 Chain D: Q.24, H.127 11 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: C:V.97, C:V.97, C:N.105, B:E.116, D:Q.24 Hydrogen bonds: C:D.13, C:G.70, C:Q.95, C:G.99, C:N.105, B:E.116 O6T.9: 27 residues within 4Å: Chain A: W.120, K.121, L.124 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, N.118, K.121, S.122, L.124, D.128 Ligands: O6T.1 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain C, Hydrophobic interactions: A:W.120, C:W.79, C:W.79, C:L.110, C:T.114, C:L.124 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.88, C:S.88, C:S.112, C:D.128 O6T.11: 18 residues within 4Å: Chain A: Q.24, H.127 Chain B: D.13, G.68, S.69, G.70, T.71, Q.95, Y.96, V.97, G.98, G.99, R.103, N.105 Chain C: T.114, T.115, E.116, A.119 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: B:V.97, B:V.97, B:N.105, C:E.116, A:Q.24 Hydrogen bonds: B:D.13, B:G.70, B:Q.95, B:G.99, B:N.105, C:E.116 O6T.13: 27 residues within 4Å: Chain B: W.120, K.121, L.124 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, N.118, K.121, S.122, L.124, D.128 Ligands: O6T.5 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:W.79, D:W.79, D:L.110, D:T.114, D:L.124, B:W.120 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:N.49, D:S.88, D:S.88, D:S.112, D:D.128 O6T.15: 18 residues within 4Å: Chain A: D.13, G.68, S.69, G.70, T.71, Q.95, Y.96, V.97, G.98, G.99, R.103, N.105 Chain B: Q.24, H.127 Chain D: T.114, T.115, E.116, A.119 11 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D, Hydrophobic interactions: A:V.97, A:V.97, A:N.105, B:Q.24, D:E.116 Hydrogen bonds: A:D.13, A:G.70, A:Q.95, A:G.99, A:N.105, D:E.116

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: R.84 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.84, A:R.84 Water bridges: A:A.50 GOL.4: 5 residues within 4Å: Chain A: V.47, G.48 Chain C: W.120, K.121 Ligands: GOL.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.121, A:G.48 Water bridges: C:W.120 GOL.6: 2 residues within 4Å: Chain B: R.84 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.84, B:R.84 Water bridges: B:A.50 GOL.8: 5 residues within 4Å: Chain B: V.47, G.48 Chain D: W.120, K.121 Ligands: GOL.6 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.121, B:G.48 Water bridges: D:W.120 GOL.10: 2 residues within 4Å: Chain C: R.84 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.84, C:R.84 Water bridges: C:A.50 GOL.12: 5 residues within 4Å: Chain A: W.120, K.121 Chain C: V.47, G.48 Ligands: GOL.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.121, C:G.48 Water bridges: A:W.120 GOL.14: 2 residues within 4Å: Chain D: R.84 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.84, D:R.84 Water bridges: D:A.50 GOL.16: 5 residues within 4Å: Chain B: W.120, K.121 Chain D: V.47, G.48 Ligands: GOL.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.121, D:G.48 Water bridges: B:W.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serrano-Plana, J. et al., Enantioselective Hydroxylation of Benzylic C(sp3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology. J.Am.Chem.Soc. (2020)

Release Date

2020-07-01

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

D
AAA

Streptavidin

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