SMTL ID : 8p5z.1

Artificial transfer hydrogenase with a Mn-5 cofactor and Streptavidin S112Y-K121M mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-tetramer

Ligands

4 x X08: 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}-[2-[(5-methylpyridin-2-yl)methylamino]ethyl]pentanamide(Non-covalent)

X08.1: 23 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, Y.112, L.124, D.128 Chain D: W.120 Ligands: MN.2, BR.3, X08.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.88, A:D.128 pi-Stacking: A:Y.112 X08.4: 24 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, Y.112, M.121, L.124, D.128 Chain C: W.120 Ligands: MN.6, X08.7, BR.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:N.49, B:S.88, B:D.128 pi-Stacking: B:Y.112 X08.7: 24 residues within 4Å: Chain B: W.120 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, Y.112, M.121, D.128 Ligands: X08.4, MN.6, MN.8, BR.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.88, C:D.128 pi-Stacking: C:Y.112 X08.11: 24 residues within 4Å: Chain A: W.120 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, Y.112, M.121, D.128 Ligands: X08.1, MN.2, MN.12, BR.13 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.50, D:W.79, D:W.79, D:W.79, D:L.110 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:N.49, D:S.88, D:D.128 pi-Stacking: D:Y.112

4 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: L.124 Chain D: M.121 Ligands: X08.1, BR.3, X08.11 No protein-ligand interaction detected (PLIP) MN.6: 5 residues within 4Å: Chain B: L.124 Chain C: M.121 Ligands: X08.4, X08.7, BR.9 No protein-ligand interaction detected (PLIP) MN.8: 4 residues within 4Å: Chain B: M.121 Chain C: L.124 Ligands: X08.7, BR.10 No protein-ligand interaction detected (PLIP) MN.12: 3 residues within 4Å: Chain D: L.124 Ligands: X08.11, BR.13 No protein-ligand interaction detected (PLIP)

4 x BR: BROMIDE ION(Non-functional Binders)

BR.3: 2 residues within 4Å: Ligands: X08.1, MN.2 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain C: M.121 Ligands: X08.4, MN.6 Ligand excluded by PLIP BR.10: 2 residues within 4Å: Ligands: X08.7, MN.8 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Ligands: X08.11, MN.12 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: Q.24, L.25, W.108, G.126, H.127, D.128 Chain C: A.119, W.120 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:A.119, B:Q.24, B:W.108, B:H.127, B:H.127 Water bridges: C:W.120, C:S.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Manganese Transfer Hydrogenases Based on the Biotin-Streptavidin Technology. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-09-13

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin