SMTL ID : 6rsj.1

Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and soaked with 25 eq. spermine - structure I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, A.86, F.87, L.99 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:V.33, A:L.37, A:I.40, A:Y.53, A:W.64, A:Y.72, A:L.73, A:F.87, A:F.87, A:F.87, A:F.87, A:L.99 Hydrogen bonds: A:G.46, A:Q.47, A:Y.53, A:T.54, A:N.57, A:T.83, A:K.84 Water bridges: A:R.43, A:A.48, A:T.83 Metal complexes: A:H.23, H2O.3

3 x EVB: sulfonato-calix[8]arene(Non-covalent)

EVB.2: 11 residues within 4Å: Chain A: K.16, T.17, L.20, Q.21, T.24, E.26, G.29, P.30, H.31, K.32 Ligands: GOL.13 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.20, A:L.20, A:L.20, A:L.20, A:L.20, A:Q.21, A:T.24, A:P.30, A:P.30, A:P.30 Hydrogen bonds: A:L.20, A:E.26, A:E.26, A:K.32, A:K.32, A:K.32 Water bridges: A:Q.21, A:Q.21, A:Q.21, A:Q.21, A:K.32 Salt bridges: A:K.16, A:K.16 EVB.3: 14 residues within 4Å: Chain A: A.5, G.6, A.8, K.9, A.12, T.101, Y.102, K.104, K.105, A.106 Ligands: SPM.5, SPM.6, SO4.7, SO4.8 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:A.5, A:K.9, A:A.12, A:T.101, A:Y.102, A:Y.102, A:K.105, A:K.105 Hydrogen bonds: A:G.6, A:A.8 Water bridges: A:G.6, A:G.6, A:A.8, A:A.8, A:K.104, A:K.104, A:K.104, A:K.104, A:K.105, A:K.105, A:K.105, A:K.105 Salt bridges: A:K.9, A:K.104, A:K.105, A:K.105 EVB.4: 13 residues within 4Å: Chain A: R.18, T.74, N.75, K.77, K.78, M.85, A.86, F.87, G.88, G.89, L.90, K.91, K.92 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:K.77, A:K.77, A:K.78, A:K.91 Hydrogen bonds: A:N.75, A:G.82, A:G.88, A:K.91, A:K.92 Water bridges: A:K.77, A:K.91, A:K.91 Salt bridges: A:R.18, A:R.18, A:K.77, A:K.77, A:K.78, A:K.78, A:K.91, A:K.92 pi-Cation interactions: A:K.77, A:K.77, A:K.91

2 x SPM: SPERMINE(Non-functional Binders)

SPM.5: 2 residues within 4Å: Ligands: EVB.3, SO4.7 No protein-ligand interaction detected (PLIP) SPM.6: 2 residues within 4Å: Ligands: EVB.3, SO4.8 No protein-ligand interaction detected (PLIP)

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

SO4.7: 2 residues within 4Å: Ligands: EVB.3, SPM.5 No protein-ligand interaction detected (PLIP) SO4.8: 2 residues within 4Å: Ligands: EVB.3, SPM.6 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: D.55, A.56, K.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.59 Water bridges: A:A.56, A:K.59, A:G.82 GOL.10: 5 residues within 4Å: Chain A: G.28, G.29, H.31, E.49, G.50 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.28, A:H.31, A:N.36 GOL.11: 4 residues within 4Å: Chain A: K.91, K.92, E.93, K.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.93, A:K.94 GOL.12: 4 residues within 4Å: Chain A: A.1, E.2, E.93, R.96 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.1, A:A.1, A:E.2, A:E.93, A:E.93, A:R.96, A:R.96 Water bridges: A:S.70 GOL.13: 3 residues within 4Å: Chain A: K.32, V.33 Ligands: EVB.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engilberge, S. et al., Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. Acs Nano (2019)

Release Date

2019-09-18

Peptides

Cytochrome c iso-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c iso-1

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