SMTL ID : 9ffj.1

Artificial metalloenzyme with a nickel-based 1,10-phenanthroline cofactor and streptavidin N49M-S112V mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: T.20, Y.22, T.28, I.30, E.44, K.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.22, A:E.44, A:K.134 EDO.5: 6 residues within 4Å: Chain A: I.30, V.31, T.32, T.40, G.41, T.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.32, A:T.40 EDO.9: 6 residues within 4Å: Chain B: T.20, Y.22, T.28, I.30, E.44, K.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.22, B:E.44, B:K.134 EDO.13: 6 residues within 4Å: Chain B: I.30, V.31, T.32, T.40, G.41, T.42 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.32, B:T.40 EDO.17: 6 residues within 4Å: Chain C: T.20, Y.22, T.28, I.30, E.44, K.134 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.22, C:E.44, C:K.134 EDO.21: 6 residues within 4Å: Chain C: I.30, V.31, T.32, T.40, G.41, T.42 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.32, C:T.40 EDO.25: 6 residues within 4Å: Chain D: T.20, Y.22, T.28, I.30, E.44, K.134 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.22, D:E.44, D:K.134 EDO.29: 6 residues within 4Å: Chain D: I.30, V.31, T.32, T.40, G.41, T.42 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.32, D:T.40

4 x 01: N-methyl-N-[(4,4,6,6-tetrahydroxy-4,6-dioxido-1,3,3a,5,6a-tetrahydrothien[3,4-d]imidazol-4-ium-2-yl)methyl]-5-(2,4,4-trihydroxy-2-keto-3,3a,5,6-tetrahydro-1H-thien[3,4-d]imidazol-4-ium-6-yl

01.2: 20 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, M.49, A.50, W.79, A.86, H.87, S.88, T.90, W.92, W.108, L.110, V.112, D.128 Chain C: W.120 18 PLIP interactions: 16 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:M.49, A:A.50, A:W.79, A:W.79, A:W.79, A:A.86, A:L.110, A:V.112 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:S.45, A:M.49, A:A.86, A:D.128 Metal complexes: 01.2, 01.2 01.10: 20 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, M.49, A.50, W.79, A.86, H.87, S.88, T.90, W.92, W.108, L.110, V.112, D.128 Chain D: W.120 17 PLIP interactions: 15 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:M.49, B:A.50, B:W.79, B:W.79, B:W.79, B:A.86, B:L.110, B:V.112 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:S.45, B:M.49, B:D.128 Metal complexes: 01.10, 01.10 01.18: 20 residues within 4Å: Chain A: W.120 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, M.49, A.50, W.79, A.86, H.87, S.88, T.90, W.92, W.108, L.110, V.112, D.128 18 PLIP interactions: 16 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:M.49, C:A.50, C:W.79, C:W.79, C:W.79, C:A.86, C:L.110, C:V.112 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:S.45, C:M.49, C:A.86, C:D.128 Metal complexes: 01.18, 01.18 01.26: 20 residues within 4Å: Chain B: W.120 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, M.49, A.50, W.79, A.86, H.87, S.88, T.90, W.92, W.108, L.110, V.112, D.128 17 PLIP interactions: 15 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:M.49, D:A.50, D:W.79, D:W.79, D:W.79, D:A.86, D:L.110, D:V.112 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:S.45, D:M.49, D:D.128 Metal complexes: 01.26, 01.26

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: T.111, E.116, A.119, S.122, T.123 Chain D: G.94, Q.95, V.97, N.105 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.95, D:N.105, A:T.123 Water bridges: A:T.114 PEG.4: 8 residues within 4Å: Chain A: A.15, G.16, W.21, Y.96, G.98, G.99, A.102, K.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.15, A:Y.96, A:G.99 PEG.11: 9 residues within 4Å: Chain B: T.111, E.116, A.119, S.122, T.123 Chain C: G.94, Q.95, V.97, N.105 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.123, C:Q.95, C:N.105 Water bridges: B:T.114 PEG.12: 8 residues within 4Å: Chain B: A.15, G.16, W.21, Y.96, G.98, G.99, A.102, K.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.15, B:Y.96, B:G.99 PEG.19: 9 residues within 4Å: Chain B: G.94, Q.95, V.97, N.105 Chain C: T.111, E.116, A.119, S.122, T.123 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.95, B:N.105, C:T.123 Water bridges: C:T.114 PEG.20: 8 residues within 4Å: Chain C: A.15, G.16, W.21, Y.96, G.98, G.99, A.102, K.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.15, C:Y.96, C:G.99 PEG.27: 9 residues within 4Å: Chain A: G.94, Q.95, V.97, N.105 Chain D: T.111, E.116, A.119, S.122, T.123 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.95, A:N.105, D:T.123 Water bridges: D:T.114 PEG.28: 8 residues within 4Å: Chain D: A.15, G.16, W.21, Y.96, G.98, G.99, A.102, K.132 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.15, D:Y.96, D:G.99

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

SO4.6: 5 residues within 4Å: Chain D: K.80, N.81, N.82, R.84, N.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.85 Salt bridges: D:K.80 SO4.7: 6 residues within 4Å: Chain A: Q.24, L.25, H.127, D.128 Chain C: W.120 Ligands: NH4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.24, A:D.128 Salt bridges: A:H.127 SO4.14: 5 residues within 4Å: Chain C: K.80, N.81, N.82, R.84, N.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.85 Salt bridges: C:K.80 SO4.15: 6 residues within 4Å: Chain B: Q.24, L.25, H.127, D.128 Chain D: W.120 Ligands: NH4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.24 Salt bridges: B:H.127 SO4.22: 5 residues within 4Å: Chain B: K.80, N.81, N.82, R.84, N.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.85 Salt bridges: B:K.80 SO4.23: 6 residues within 4Å: Chain A: W.120 Chain C: Q.24, L.25, H.127, D.128 Ligands: NH4.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.24, C:D.128 Salt bridges: C:H.127 SO4.30: 5 residues within 4Å: Chain A: K.80, N.81, N.82, R.84, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85 Salt bridges: A:K.80 SO4.31: 6 residues within 4Å: Chain B: W.120 Chain D: Q.24, L.25, H.127, D.128 Ligands: NH4.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.24 Salt bridges: D:H.127

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.8: 6 residues within 4Å: Chain A: W.108, G.126, H.127 Chain B: Q.107 Chain C: W.120 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.127, A:H.127 NH4.16: 6 residues within 4Å: Chain A: Q.107 Chain B: W.108, G.126, H.127 Chain D: W.120 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.127, B:H.127 NH4.24: 6 residues within 4Å: Chain A: W.120 Chain C: W.108, G.126, H.127 Chain D: Q.107 Ligands: SO4.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.127, C:H.127 NH4.32: 6 residues within 4Å: Chain B: W.120 Chain C: Q.107 Chain D: W.108, G.126, H.127 Ligands: SO4.31 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.127, D:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Artificial Metalloenzymes with Two Catalytic Cofactors for Tandem Abiotic Transformations. Angew.Chem.Int.Ed.Engl. (2025)

Release Date

2025-01-15

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin