SMTL ID : 6t30.1

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: 21 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, S.112, A.121, S.122, L.124, D.128 Chain D: W.120 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.124 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:K.49, A:S.88, A:S.88, A:D.128 Water bridges: A:S.112 HL9.4: 20 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, S.112, A.121, L.124, D.128 Chain C: W.120 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:A.86, B:L.110, C:W.120 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:K.49, B:S.88, B:S.88, B:D.128 HL9.7: 21 residues within 4Å: Chain B: W.120 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, S.112, A.121, S.122, L.124, D.128 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.124 Hydrogen bonds: C:N.23, C:S.27, C:S.45, C:K.49, C:S.88, C:S.88, C:D.128 Water bridges: C:S.112 HL9.10: 20 residues within 4Å: Chain A: 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, S.112, A.121, L.124, D.128 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:A.86, D:L.110, A:W.120 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:K.49, D:S.88, D:S.88, D:D.128

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

EDO.2: 2 residues within 4Å: Chain A: A.65, T.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.66 EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain B: T.115, G.119 Chain D: Q.95, V.97, N.105 Ligands: GOL.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.105, B:T.115 Water bridges: D:Q.95 EDO.8: 2 residues within 4Å: Chain C: A.65, T.66 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.66 EDO.9: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.20, C:T.20 EDO.11: 6 residues within 4Å: Chain B: Q.95, V.97, N.105 Chain D: T.115, G.119 Ligands: GOL.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.105, D:T.115 Water bridges: B:Q.95

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: H.127 Chain B: N.105, T.106, Q.107 Chain D: G.119, S.122, T.123 Ligands: EDO.11 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: B:N.105, D:T.123 Water bridges: B:Q.107, A:V.125, D:S.122, D:T.123 GOL.12: 8 residues within 4Å: Chain B: G.119, S.122, T.123 Chain C: H.127 Chain D: N.105, T.106, Q.107 Ligands: EDO.5 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:N.105, B:T.123 Water bridges: D:Q.107, B:W.120, B:S.122, B:T.123

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
B

B
A

C
B

D
A

Streptavidin