SMTL ID : 6suy.1

Yeast cytochrome c in complex with an octa-anionic calix[4]arene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: R.18, C.19, Q.21, C.22, H.23, V.33, G.34, P.35, 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 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Q.21, A:V.33, A:P.35, A:I.40, A:Y.51, A:L.73, A:M.85, A:F.87, A:F.87, A:F.87, A:L.99, A:L.99 Hydrogen bonds: A:G.46, A:T.54, A:N.57, A:T.83, A:K.84 Water bridges: A:Q.47, A:A.48, A:T.83 Salt bridges: A:K.84 pi-Stacking: A:Y.72 Metal complexes: A:H.23 HEC.8: 27 residues within 4Å: Chain B: 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, L.103 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:Q.21, B:V.33, B:P.35, B:L.37, B:I.40, B:Y.51, B:W.64, B:Y.72, B:L.73, B:M.85, B:F.87, B:L.103 Hydrogen bonds: B:G.46, B:Y.53, B:T.54, B:N.57, B:T.83, B:K.84 Water bridges: B:R.43, B:Q.47, B:A.48, B:T.83 pi-Stacking: B:Y.72 Metal complexes: B:H.23

2 x LVT: octa-anionic calix[4]arene(Non-covalent)

LVT.2: 8 residues within 4Å: Chain A: R.18, F.87, G.88, G.89, L.90, K.91, K.92 Ligands: NA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.91 Hydrogen bonds: A:G.88, A:G.89, A:K.91, A:K.92 Water bridges: A:A.86, A:D.95, A:D.95 Salt bridges: A:R.18, A:R.18, A:K.92 LVT.9: 4 residues within 4Å: Chain B: K.92, E.93, K.94 Ligands: NA.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.94, B:K.94 Hydrogen bonds: B:E.93, B:K.94 Water bridges: B:K.92 Salt bridges: B:K.92

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Ligands: LVT.2 No protein-ligand interaction detected (PLIP) NA.10: 1 residues within 4Å: Ligands: LVT.9 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: T.74, N.75, K.78, K.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75 Salt bridges: A:K.91 SO4.5: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.82 SO4.6: 2 residues within 4Å: Chain A: T.13, K.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.13, A:K.16 Salt bridges: A:K.16 SO4.7: 3 residues within 4Å: Chain A: S.7, A.8, K.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.8, A:K.9 Salt bridges: A:K.9 SO4.11: 4 residues within 4Å: Chain B: T.74, N.75, K.78, K.91 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.75 Water bridges: B:K.78, B:K.78 Salt bridges: B:K.78, B:K.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alex, J.M. et al., Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org.Biomol.Chem. (2020)

Release Date

2020-01-15

Peptides

Cytochrome c iso-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c iso-1

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