SMTL ID : 6t1e.1

Streptavidin variants harbouring an artificial organocatalyst based cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) GOL.2: 4 residues within 4Å: Chain A: G.48, K.49, R.84 Ligands: ACT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.49, A:R.84, A:R.84 GOL.3: 7 residues within 4Å: Chain A: D.36, R.59, S.62 Chain D: V.55, K.80, N.81, N.82 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:K.80, D:N.82, A:R.59, A:S.62 Water bridges: A:R.59, A:S.62 GOL.7: 6 residues within 4Å: Chain B: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain B: G.48, K.49, R.84 Ligands: ACT.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.49, B:R.84, B:R.84 GOL.9: 7 residues within 4Å: Chain B: D.36, R.59, S.62 Chain C: V.55, K.80, N.81, N.82 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.80, C:N.82, B:R.59, B:S.62 Water bridges: B:R.59, B:S.62 GOL.13: 6 residues within 4Å: Chain C: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) GOL.14: 4 residues within 4Å: Chain C: G.48, K.49, R.84 Ligands: ACT.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.49, C:R.84, C:R.84 GOL.15: 7 residues within 4Å: Chain B: V.55, K.80, N.81, N.82 Chain C: D.36, R.59, S.62 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.80, B:N.82, C:R.59, C:S.62 Water bridges: C:R.59, C:S.62 GOL.19: 6 residues within 4Å: Chain D: K.80, N.81, N.82, Y.83, R.84, N.85 No protein-ligand interaction detected (PLIP) GOL.20: 4 residues within 4Å: Chain D: G.48, K.49, R.84 Ligands: ACT.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.49, D:R.84, D:R.84 GOL.21: 7 residues within 4Å: Chain A: V.55, K.80, N.81, N.82 Chain D: D.36, R.59, S.62 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.59, D:S.62, A:K.80, A:N.82 Water bridges: D:R.59, D:S.62

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: G.48, K.49 Chain C: N.118, W.120, R.121 Ligands: GOL.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.48, A:G.48 Water bridges: A:K.49 Salt bridges: A:K.49, C:R.121 Hydrophobic interactions: C:W.120 ACT.10: 6 residues within 4Å: Chain B: G.48, K.49 Chain D: N.118, W.120, R.121 Ligands: GOL.8 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.48, B:G.48 Water bridges: B:K.49 Salt bridges: B:K.49, D:R.121 Hydrophobic interactions: D:W.120 ACT.16: 6 residues within 4Å: Chain A: N.118, W.120, R.121 Chain C: G.48, K.49 Ligands: GOL.14 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:W.120 Salt bridges: A:R.121, C:K.49 Hydrogen bonds: C:G.48, C:G.48 Water bridges: C:K.49 ACT.22: 6 residues within 4Å: Chain B: N.118, W.120, R.121 Chain D: G.48, K.49 Ligands: GOL.20 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.48, D:G.48 Water bridges: D:K.49 Salt bridges: D:K.49, B:R.121 Hydrophobic interactions: B:W.120

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)

HL9.5: 23 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, S.112, Q.114, R.121, L.124, D.128 Chain C: W.120 Ligands: CL.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.49, A:W.79, A:W.79, A:W.79 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:K.49, A:S.88, A:Q.114, A:D.128 Water bridges: A:R.121 HL9.11: 23 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, S.112, Q.114, R.121, L.124, D.128 Chain D: W.120 Ligands: CL.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:K.49, B:W.79, B:W.79, B:W.79 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:K.49, B:S.88, B:Q.114, B:D.128 Water bridges: B:R.121 HL9.17: 23 residues within 4Å: Chain A: W.120 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, S.112, Q.114, R.121, L.124, D.128 Ligands: CL.18 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.49, C:W.79, C:W.79, C:W.79 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:K.49, C:S.88, C:Q.114, C:D.128 Water bridges: C:R.121 HL9.23: 23 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, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, Q.114, R.121, L.124, D.128 Ligands: CL.24 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:K.49, 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:Q.114, D:D.128 Water bridges: D:R.121

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: Q.114, R.121 Ligands: HL9.5 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: Q.114, R.121 Ligands: HL9.11 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: Q.114, R.121 Ligands: HL9.17 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: Q.114, R.121 Ligands: HL9.23 Ligand excluded by PLIP

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

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