SMTL ID : 8ojx.1

Streptavidin S112YK121E artificial metalloenzyme for carboamination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x 0OD: trichloro{(1,2,3,4,5-eta)-1,2,3,4-tetramethyl-5-[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]cyclopentadienyl}rhodium(1+)(Non-covalent)

0OD.1: 22 residues within 4Å: Chain A: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, Y.100, L.112, D.116 Chain C: Y.100, W.108, E.109 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.38, A:W.67, A:W.67, A:W.67, A:L.98, A:Y.100, A:Y.100, C:W.108, C:W.108 Hydrogen bonds: A:N.11, A:S.15, A:S.33, A:N.37, A:S.76, A:S.76, A:D.116 0OD.5: 22 residues within 4Å: Chain B: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, Y.100, L.112, D.116 Chain D: Y.100, W.108, E.109 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:A.38, B:W.67, B:W.67, B:W.67, B:L.98, B:Y.100, B:Y.100, D:W.108, D:W.108 Hydrogen bonds: B:N.11, B:S.15, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 0OD.9: 22 residues within 4Å: Chain A: Y.100, W.108, E.109 Chain C: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, Y.100, L.112, D.116 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.38, C:W.67, C:W.67, C:W.67, C:L.98, C:Y.100, C:Y.100, A:W.108, A:W.108 Hydrogen bonds: C:N.11, C:S.15, C:S.33, C:N.37, C:S.76, C:S.76, C:D.116 0OD.13: 22 residues within 4Å: Chain B: Y.100, W.108, E.109 Chain D: N.11, L.13, S.15, Y.31, S.33, V.35, G.36, N.37, A.38, W.67, A.74, S.76, T.78, W.80, W.96, L.98, Y.100, L.112, D.116 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:A.38, D:W.67, D:W.67, D:W.67, D:L.98, D:Y.100, D:Y.100, B:W.108, B:W.108 Hydrogen bonds: D:N.11, D:S.15, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

12 x IR: IRIDIUM ION(Non-covalent)

IR.2: 2 residues within 4Å: Chain A: H.75 Chain D: A.53 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.75 IR.3: 2 residues within 4Å: Chain A: H.115 Chain B: N.93 No protein-ligand interaction detected (PLIP) IR.4: 3 residues within 4Å: Chain A: H.115 Chain B: H.115 Ligands: IR.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.115, H2O.3, H2O.4 IR.6: 2 residues within 4Å: Chain B: H.75 Chain C: A.53 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.75 IR.7: 2 residues within 4Å: Chain A: N.93 Chain B: H.115 No protein-ligand interaction detected (PLIP) IR.8: 3 residues within 4Å: Chain A: H.115 Chain B: H.115 Ligands: IR.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.115, H2O.1, H2O.6 IR.10: 2 residues within 4Å: Chain B: A.53 Chain C: H.75 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.75 IR.11: 2 residues within 4Å: Chain C: H.115 Chain D: N.93 No protein-ligand interaction detected (PLIP) IR.12: 3 residues within 4Å: Chain C: H.115 Chain D: H.115 Ligands: IR.16 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.115, H2O.9, H2O.11 IR.14: 2 residues within 4Å: Chain A: A.53 Chain D: H.75 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.75 IR.15: 2 residues within 4Å: Chain C: N.93 Chain D: H.115 No protein-ligand interaction detected (PLIP) IR.16: 3 residues within 4Å: Chain C: H.115 Chain D: H.115 Ligands: IR.12 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.115, H2O.8, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igareta, N.V., Streptavidin WT artificial metalloenzyme for carboamination. To Be Published

Release Date

2024-04-03

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin