SMTL ID : 6t2l.1

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-tetramer

Ligands

4 x HL9: 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide(Non-covalent)

HL9.1: 24 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, T.123, L.124, D.128 Chain C: W.120, L.124 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:A.112, A:L.124 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:K.49, A:S.88, A:D.128 HL9.4: 24 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, T.123, L.124, D.128 Chain D: W.120, L.124 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:A.112, B:L.124 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:K.49, B:S.88, B:D.128 HL9.7: 24 residues within 4Å: Chain A: W.120, L.124 Chain C: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, T.123, L.124, D.128 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:A.112, C:L.124 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:K.49, C:S.88, C:D.128 HL9.10: 24 residues within 4Å: Chain B: W.120, L.124 Chain D: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, T.123, L.124, D.128 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:A.112, D:L.124 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:K.49, D:S.88, D:D.128

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain B: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain C: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain D: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: D.36, R.59, S.62 Chain D: V.55, K.80, N.81, N.82 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.62, A:S.62, D:K.80 Water bridges: A:D.36, A:R.59, A:R.59, A:S.62, D:V.55, D:K.80 GOL.6: 7 residues within 4Å: Chain B: D.36, R.59, S.62 Chain C: V.55, K.80, N.81, N.82 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.62, B:S.62, C:K.80 Water bridges: B:R.59, B:R.59, B:S.62, C:V.55, C:K.80 GOL.9: 7 residues within 4Å: Chain B: V.55, K.80, N.81, N.82 Chain C: D.36, R.59, S.62 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:K.80, C:S.62, C:S.62 Water bridges: B:V.55, B:K.80, C:D.36, C:R.59, C:R.59, C:S.62 GOL.12: 7 residues within 4Å: Chain A: V.55, K.80, N.81, N.82 Chain D: D.36, R.59, S.62 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:S.62, D:S.62, A:K.80 Water bridges: D:R.59, D:R.59, D:S.62, A:V.55, A:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lechner, H. et al., An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*. Chembiochem (2021)

Release Date

2020-10-14

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin