SMTL ID : 8b7l.1

X-ray structure of Auranofin-horse spleen ferritin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-trimer

Ligands

27 x CD: CADMIUM ION(Non-covalent)

CD.1: 1 residues within 4Å: Chain A: H.132 Ligand excluded by PLIP CD.4: 5 residues within 4Å: Chain A: D.127 Chain B: D.127 Chain C: D.127 Ligands: CD.18, CD.32 Ligand excluded by PLIP CD.5: 5 residues within 4Å: Chain A: E.130 Chain B: E.130 Chain C: E.130 Ligands: CD.19, CD.33 Ligand excluded by PLIP CD.6: 3 residues within 4Å: Chain A: E.56, E.57, E.60 Ligand excluded by PLIP CD.7: 2 residues within 4Å: Chain A: F.50, H.147 Ligand excluded by PLIP CD.8: 1 residues within 4Å: Chain A: D.80 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: E.53, E.56 Ligand excluded by PLIP CD.10: 3 residues within 4Å: Chain A: C.48, H.49, R.52 Ligand excluded by PLIP CD.11: 1 residues within 4Å: Chain A: E.11 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Chain B: H.132 Ligand excluded by PLIP CD.18: 5 residues within 4Å: Chain A: D.127 Chain B: D.127 Chain C: D.127 Ligands: CD.4, CD.32 Ligand excluded by PLIP CD.19: 5 residues within 4Å: Chain A: E.130 Chain B: E.130 Chain C: E.130 Ligands: CD.5, CD.33 Ligand excluded by PLIP CD.20: 3 residues within 4Å: Chain B: E.56, E.57, E.60 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain B: F.50, H.147 Ligand excluded by PLIP CD.22: 1 residues within 4Å: Chain B: D.80 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain B: E.53, E.56 Ligand excluded by PLIP CD.24: 3 residues within 4Å: Chain B: C.48, H.49, R.52 Ligand excluded by PLIP CD.25: 1 residues within 4Å: Chain B: E.11 Ligand excluded by PLIP CD.29: 1 residues within 4Å: Chain C: H.132 Ligand excluded by PLIP CD.32: 5 residues within 4Å: Chain A: D.127 Chain B: D.127 Chain C: D.127 Ligands: CD.4, CD.18 Ligand excluded by PLIP CD.33: 5 residues within 4Å: Chain A: E.130 Chain B: E.130 Chain C: E.130 Ligands: CD.5, CD.19 Ligand excluded by PLIP CD.34: 3 residues within 4Å: Chain C: E.56, E.57, E.60 Ligand excluded by PLIP CD.35: 2 residues within 4Å: Chain C: F.50, H.147 Ligand excluded by PLIP CD.36: 1 residues within 4Å: Chain C: D.80 Ligand excluded by PLIP CD.37: 2 residues within 4Å: Chain C: E.53, E.56 Ligand excluded by PLIP CD.38: 3 residues within 4Å: Chain C: C.48, H.49, R.52 Ligand excluded by PLIP CD.39: 1 residues within 4Å: Chain C: E.11 Ligand excluded by PLIP

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

SO4.2: 2 residues within 4Å: Chain A: Q.6, N.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.108, A:N.7 Hydrogen bonds: A:N.7 SO4.16: 2 residues within 4Å: Chain B: Q.6, N.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:Q.108, B:N.7 Hydrogen bonds: B:N.7 SO4.30: 2 residues within 4Å: Chain C: Q.6, N.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:Q.108, C:N.7 Hydrogen bonds: C:N.7

3 x AU: GOLD ION(Non-covalent)

AU.3: 5 residues within 4Å: Chain A: G.117, S.118, D.122, P.123, C.126 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.126, H2O.10 AU.17: 5 residues within 4Å: Chain B: G.117, S.118, D.122, P.123, C.126 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.126, H2O.23 AU.31: 5 residues within 4Å: Chain C: G.117, S.118, D.122, P.123, C.126 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.126, H2O.36

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

CL.12: 1 residues within 4Å: Chain A: Q.82 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: E.45 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: L.169 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain B: Q.82 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: E.45 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain B: L.169 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain C: Q.82 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain C: E.45 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain C: L.169 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucignano, R. et al., Evaluation of Auranofin Loading within Ferritin Nanocages. Int J Mol Sci (2022)

Release Date

2022-12-28

Peptides

Ferritin light chain: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

Ferritin light chain

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