SMTL ID : 6t2y.1

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: V.55, K.80, N.81, N.82 Chain B: R.59 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.59, A:K.80, A:N.82 Water bridges: B:R.59, A:V.55, A:K.80 EDO.3: 4 residues within 4Å: Chain A: N.105, T.106, Q.107 Chain D: H.127 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:S.93, D:H.127 Water bridges: A:T.106, B:T.123 EDO.5: 5 residues within 4Å: Chain A: T.123 Chain B: N.105, T.106, Q.107 Chain C: H.127 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:N.105, A:T.123 Water bridges: B:Q.107, C:H.127, A:S.122 EDO.6: 5 residues within 4Å: Chain C: V.55, K.80, N.81, N.82 Chain D: R.59 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.80, C:N.82, D:R.59 Water bridges: C:V.55, C:K.80, D:R.59 EDO.8: 4 residues within 4Å: Chain B: H.127 Chain C: N.105, T.106, Q.107 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.93, B:H.127 Water bridges: C:T.106, C:Q.107 EDO.10: 5 residues within 4Å: Chain A: H.127 Chain C: T.123 Chain D: N.105, T.106, Q.107 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Water bridges: C:S.122, D:Q.107, A:H.127 Hydrogen bonds: D:N.105

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)

HL9.2: 22 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, Y.124, D.128 Chain C: W.120, Y.124 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:A.112 Hydrogen bonds: A:N.23, A:S.27, A:S.45, A:K.49, A:S.88, A:S.88, A:D.128 HL9.4: 21 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, Y.124, D.128 Chain D: W.120 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:W.79 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:K.49, B:S.88, B:S.88, B:D.128 HL9.7: 22 residues within 4Å: Chain A: W.120, Y.124 Chain C: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, Y.124, D.128 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:A.112 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:K.49, C:S.88, C:S.88, C:D.128 HL9.9: 21 residues within 4Å: Chain B: W.120 Chain D: N.23, L.25, S.27, Y.43, S.45, A.47, G.48, K.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, A.121, S.122, Y.124, D.128 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79, D:W.79 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:K.49, D:S.88, D:S.88, D:D.128

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

2020-11-18

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin