SMTL ID : 5f2b.1

Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x 9RU: [1-[4-[[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]pentanoylamino]methyl]-2,6-dimethyl-phenyl]-3-(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-1-ium-2-yl]-bis(chloranyl)ruthenium(Non-covalent)

9RU.1: 24 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, Q.114, R.121, L.124, D.128 Chain C: W.120, R.121, L.124 Ligands: 9RU.5 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:L.124, A:L.124, C:W.120, C:R.121 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 9RU.3: 24 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, Q.114, R.121, L.124, D.128 Chain D: W.120, R.121, L.124 Ligands: 9RU.7 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:L.124, B:L.124, D:W.120, D:R.121 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:K.49, B:S.88, B:S.88, B:D.128 9RU.5: 24 residues within 4Å: Chain A: W.120, R.121, L.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, S.112, Q.114, R.121, L.124, D.128 Ligands: 9RU.1 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:L.124, C:L.124, A:W.120, A:R.121 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 9RU.7: 24 residues within 4Å: Chain B: W.120, R.121, L.124 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, Q.114, R.121, L.124, D.128 Ligands: 9RU.3 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:L.124, D:L.124, B:W.120, B:R.121 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:K.49, D:S.88, D:S.88, D:D.128

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: G.34, A.35, D.36, G.37, A.38, R.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.35, A:D.36, A:A.38, A:R.59 SO4.4: 6 residues within 4Å: Chain B: G.34, A.35, D.36, G.37, A.38, R.59 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.35, B:D.36, B:D.36, B:A.38, B:R.59 SO4.6: 6 residues within 4Å: Chain C: G.34, A.35, D.36, G.37, A.38, R.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.35, C:D.36, C:A.38, C:R.59 SO4.8: 6 residues within 4Å: Chain D: G.34, A.35, D.36, G.37, A.38, R.59 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.35, D:D.36, D:D.36, D:A.38, D:R.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeschek, M. et al., Directed evolution of artificial metalloenzymes for in vivo metathesis. Nature (2016)

Release Date

2016-08-31

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

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