SMTL ID : 6t1k.1

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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, Q.114, A.121, S.122, 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 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:K.49, A:S.88, A:D.128 Water bridges: A:Q.114 HL9.5: 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, Q.114, A.121, S.122, 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 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:K.49, B:S.88, B:D.128 Water bridges: B:Q.114 HL9.9: 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, Q.114, 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:A.112 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:K.49, C:S.88, C:D.128 Water bridges: C:Q.114 HL9.13: 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, Q.114, A.121, S.122, 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 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:K.49, D:S.88, D:D.128 Water bridges: D:Q.114

12 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.84, A:R.84 EDO.3: 6 residues within 4Å: Chain A: D.36, R.59 Chain D: V.55, K.80, N.81 Ligands: EDO.16 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:K.80, A:R.59, A:R.59 Water bridges: D:K.80, A:R.59 EDO.4: 7 residues within 4Å: Chain A: T.42, R.53, Y.54, V.55, N.81, N.82 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.53 Water bridges: A:V.55, A:N.82 EDO.6: 6 residues within 4Å: Chain B: K.80, N.81, N.82, Y.83, R.84, N.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.84, B:R.84 EDO.7: 6 residues within 4Å: Chain B: D.36, R.59 Chain C: V.55, K.80, N.81 Ligands: EDO.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.59, B:R.59, C:K.80 Water bridges: B:R.59, C:K.80 EDO.8: 7 residues within 4Å: Chain B: T.42, R.53, Y.54, V.55, N.81, N.82 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.53 Water bridges: B:V.55, B:N.82 EDO.10: 6 residues within 4Å: Chain C: K.80, N.81, N.82, Y.83, R.84, N.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.84, C:R.84 EDO.11: 6 residues within 4Å: Chain B: V.55, K.80, N.81 Chain C: D.36, R.59 Ligands: EDO.8 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.59, C:R.59, B:K.80 Water bridges: C:R.59, B:K.80 EDO.12: 7 residues within 4Å: Chain C: T.42, R.53, Y.54, V.55, N.81, N.82 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.53 Water bridges: C:V.55, C:N.82 EDO.14: 6 residues within 4Å: Chain D: K.80, N.81, N.82, Y.83, R.84, N.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.84, D:R.84 EDO.15: 6 residues within 4Å: Chain A: V.55, K.80, N.81 Chain D: D.36, R.59 Ligands: EDO.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:K.80, D:R.59, D:R.59 Water bridges: A:K.80, D:R.59 EDO.16: 7 residues within 4Å: Chain D: T.42, R.53, Y.54, V.55, N.81, N.82 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.53 Water bridges: D:V.55, D:N.82

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