SMTL ID : 8p5y.1

Artificial transfer hydrogenase with a Mn-12 cofactor and Streptavidin S112Y-K121M mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x WZQ: 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-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)ethyl]pentanamide(Non-covalent)

WZQ.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, M.121, D.128 Chain D: W.120 Ligands: MN.2, BR.4, WZQ.11 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, D:W.120, D:W.120 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 WZQ.5: 23 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, D.128 Chain C: W.120 Ligands: MN.6, WZQ.8, BR.9 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:Y.112, C:W.120 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:N.49, B:S.88, B:W.92, B:D.128 Water bridges: B:S.88 pi-Stacking: B:Y.112 WZQ.8: 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: WZQ.5, MN.6, MN.7, BR.10 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.50, 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 WZQ.11: 23 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: WZQ.1, MN.3, BR.12 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, D:Y.112 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:N.49, D:S.88, D:D.128

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

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

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

BR.4: 3 residues within 4Å: Chain A: N.49 Ligands: WZQ.1, MN.2 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain C: M.121 Ligands: WZQ.5, MN.6 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain C: N.49 Ligands: MN.7, WZQ.8 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain D: N.49 Ligands: MN.3, WZQ.11 Ligand excluded by PLIP

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

CL.13: 1 residues within 4Å: Chain D: R.84 Ligand excluded by PLIP

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