SMTL ID : 7pr4.1

Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: R.18, C.19, Q.21, 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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:V.33, A:P.35, A:L.37, A:I.40, A:Y.51, A:W.64, A:L.73, A:M.85, A:F.87 Hydrogen bonds: A:G.46, A:Y.53, A:T.54, A:N.57, A:T.83, A:K.84 Water bridges: A:R.43, A:Q.47, A:A.48, A:T.83 Salt bridges: A:K.84 pi-Stacking: A:Y.72 Metal complexes: A:H.23

1 x 80M: sulfonato-thiacalix[4]arene(Non-covalent)

80M.2: 10 residues within 4Å: Chain A: S.7, A.8, K.9, K.10 Ligands: ZN.3, ZN.4, ZN.5, ZN.6, PO4.9, PO4.10 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.7, A:S.7, A:S.7, A:A.8, A:K.9, A:K.10 Water bridges: A:K.9, A:K.9, A:T.13 Salt bridges: A:K.9, A:K.9, A:K.9, A:K.10 pi-Cation interactions: A:K.9, A:K.9, A:K.9, A:K.9

6 x ZN: ZINC ION(Non-functional Binders)

ZN.3: 6 residues within 4Å: Ligands: 80M.2, ZN.4, ZN.6, PO4.9, PO4.10, PO4.11 No protein-ligand interaction detected (PLIP) ZN.4: 5 residues within 4Å: Ligands: 80M.2, ZN.3, ZN.5, PO4.9, PO4.10 No protein-ligand interaction detected (PLIP) ZN.5: 4 residues within 4Å: Ligands: 80M.2, ZN.4, ZN.6, PO4.9 No protein-ligand interaction detected (PLIP) ZN.6: 4 residues within 4Å: Ligands: 80M.2, ZN.3, ZN.5, PO4.9 No protein-ligand interaction detected (PLIP) ZN.7: 3 residues within 4Å: Ligands: PO4.9, PO4.10, PO4.11 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Ligands: PO4.10, PO4.11 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 8 residues within 4Å: Ligands: 80M.2, ZN.3, ZN.4, ZN.5, ZN.6, ZN.7, PO4.10, PO4.11 No protein-ligand interaction detected (PLIP) PO4.10: 7 residues within 4Å: Ligands: 80M.2, ZN.3, ZN.4, ZN.7, ZN.8, PO4.9, PO4.11 No protein-ligand interaction detected (PLIP) PO4.11: 5 residues within 4Å: Ligands: ZN.3, ZN.7, ZN.8, PO4.9, PO4.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flood, R.J. et al., Protein Frameworks with Thiacalixarene and Zinc. Cryst.Growth Des. (2022)

Release Date

2022-03-02

Peptides

Cytochrome c iso-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c iso-1

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