SMTL ID : 8gog.1

Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x RH3: RHODIUM(III) ION(Non-covalent)

RH3.1: 2 residues within 4Å: Chain A: H.75 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.75 RH3.3: 3 residues within 4Å: Chain A: H.115 Ligands: CL.7, RH3.27 No protein-ligand interaction detected (PLIP) RH3.12: 2 residues within 4Å: Chain B: H.75 Ligands: CL.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.75 RH3.13: 3 residues within 4Å: Chain B: H.115 Ligands: CL.15, RH3.37 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.115 RH3.25: 2 residues within 4Å: Chain C: H.75 Ligands: CL.30 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.75 RH3.27: 3 residues within 4Å: Chain C: H.115 Ligands: RH3.3, CL.31 No protein-ligand interaction detected (PLIP) RH3.36: 2 residues within 4Å: Chain D: H.75 Ligands: CL.29 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.75 RH3.37: 3 residues within 4Å: Chain D: H.115 Ligands: RH3.13, CL.39 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.115

4 x JSU: trichloro((3~{a}~{S},4~{S},6~{a}~{R})-4-[(5~{R})-5-oxidanyl-5-[2-(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-ylidene)ethylamino]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-one)rhodium(3+)(Non-covalent)

JSU.2: 20 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, D.116 Chain D: W.108, E.109 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.37, A:A.38, A:W.67, A:W.67, A:W.67, A:L.98, A:Y.100 Hydrogen bonds: A:N.11, A:S.15, A:Y.31, A:S.33, A:N.37, A:S.76, A:S.76, A:D.116 JSU.14: 21 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 C: W.108, E.109 18 PLIP interactions: 2 interactions with chain C, 16 interactions with chain B Hydrophobic interactions: C:W.108, C:W.108, B:A.38, B:W.67, B:W.67, B:W.67, B:L.98, B:L.98, B:Y.100, B:Y.100, B:L.112 Hydrogen bonds: B:N.11, B:S.15, B:S.33, B:N.37, B:S.76, B:S.76, B:D.116 JSU.26: 20 residues within 4Å: Chain B: 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, D.116 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:N.37, C:A.38, C:W.67, C:W.67, C:W.67, C:L.98, C:Y.100 Hydrogen bonds: C:N.11, C:S.15, C:S.33, C:N.37, C:S.76, C:S.76, C:D.116 JSU.38: 21 residues within 4Å: Chain A: 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 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.38, D:W.67, D:W.67, D:W.67, D:L.98, D:L.98, D:Y.100, D:Y.100, D:L.112, A:W.108, A:W.108 Hydrogen bonds: D:N.11, D:S.15, D:Y.31, D:S.33, D:N.37, D:S.76, D:S.76, D:D.116

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.14, S.15, T.16, E.32, A.34 Ligand excluded by PLIP GOL.8: 1 residues within 4Å: Chain A: V.43 Ligand excluded by PLIP GOL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.16: 1 residues within 4Å: Chain B: V.43 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain B: Q.12, L.13, G.14 Ligand excluded by PLIP GOL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.19: 1 residues within 4Å: Chain B: D.24 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: T.30, V.43, N.69, N.70 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain A: V.43, T.45 Chain B: A.26, L.27, T.45, G.46, R.47 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: G.14, S.15, T.16, E.32, A.34 Ligand excluded by PLIP GOL.32: 1 residues within 4Å: Chain C: V.43 Ligand excluded by PLIP GOL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.40: 1 residues within 4Å: Chain D: V.43 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain D: Q.12, L.13, G.14 Ligand excluded by PLIP GOL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.43: 1 residues within 4Å: Chain D: D.24 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: T.30, V.43, N.69, N.70 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain C: V.43, T.45 Chain D: A.26, L.27, T.45, G.46, R.47 Ligand excluded by PLIP

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

CL.5: 1 residues within 4Å: Ligands: RH3.12 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.75 Chain B: A.51 Ligands: RH3.1 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: T.117 Ligands: RH3.3 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: H.115 Ligands: RH3.13 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Ligands: RH3.36 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: H.75 Chain D: A.51 Ligands: RH3.25 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain A: T.117 Ligands: RH3.27 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain D: H.115 Ligands: RH3.37 Ligand excluded by PLIP

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

SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.11: 1 residues within 4Å: Chain A: K.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.68 SO4.22: 1 residues within 4Å: Chain B: R.91 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.91 SO4.23: 2 residues within 4Å: Chain B: G.56, S.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.56 SO4.24: 3 residues within 4Å: Chain A: D.24, S.50 Chain B: K.68 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.50 Salt bridges: B:K.68 SO4.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.35: 1 residues within 4Å: Chain C: K.68 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.68 SO4.46: 1 residues within 4Å: Chain D: R.91 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.91 SO4.47: 2 residues within 4Å: Chain D: G.56, S.57 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.56 SO4.48: 3 residues within 4Å: Chain C: D.24, S.50 Chain D: K.68 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.50 Salt bridges: D:K.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, P. et al., Enantiodivergent synthesis of isoindolones catalysed by a Rh(III)-based artificial metalloenzyme. Nat Synth (2024)

Release Date

2024-02-28

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Streptavidin