SMTL ID : 7bbt.1

Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, R.43, 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 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.37, A:I.40, A:Y.51, A:Y.72, A:L.73, A:K.84, A:M.85, A:A.86, A:F.87, A:L.99, A:L.99, A:L.103 Hydrogen bonds: A:R.43, A:G.46, A:Y.53, A:T.54, A:N.57, A:N.57, A:T.83, A:K.84 Salt bridges: A:K.84 pi-Stacking: A:Y.72 Metal complexes: A:H.23 HEC.2: 26 residues within 4Å: Chain B: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, R.43, 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 B, Hydrophobic interactions: B:L.37, B:L.37, B:I.40, B:Y.51, B:Y.72, B:L.73, B:K.84, B:M.85, B:F.87, B:L.99, B:L.99 Hydrogen bonds: B:R.43, B:G.46, B:Y.53, B:T.54, B:N.57, B:N.57, B:T.83, B:K.84 Salt bridges: B:K.84 pi-Stacking: B:Y.72 Metal complexes: B:H.23 HEC.3: 27 residues within 4Å: Chain C: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, R.43, 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 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.37, C:I.40, C:Y.51, C:Y.72, C:L.73, C:K.84, C:M.85, C:F.87, C:L.99, C:L.99, C:L.103 Hydrogen bonds: C:R.43, C:G.46, C:T.54, C:N.57, C:N.57, C:T.83, C:T.83, C:K.84 Salt bridges: C:K.84 pi-Stacking: C:Y.72 Metal complexes: C:H.23 HEC.6: 27 residues within 4Å: Chain D: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, R.43, 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 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:L.37, D:I.40, D:Y.51, D:Y.72, D:L.73, D:K.84, D:M.85, D:A.86, D:F.87, D:L.99, D:L.99, D:L.103 Hydrogen bonds: D:R.43, D:G.46, D:Y.53, D:T.54, D:N.57, D:N.57, D:T.83, D:K.84 Salt bridges: D:K.84 pi-Stacking: D:Y.72 Metal complexes: D:H.23

3 x T8W: 4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate(Non-covalent)

T8W.4: 14 residues within 4Å: Chain C: K.10, T.13, K.16, T.17, K.92 Chain D: K.10, T.13, K.16, T.17, R.18, L.20 Ligands: T8W.5, T8W.7, 15P.8 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:T.13, D:K.16, D:T.17, D:T.17, D:L.20, C:T.13, C:K.16, C:T.17 Hydrogen bonds: D:R.18 Salt bridges: D:K.10, D:K.16, D:K.92, C:K.10, C:K.16, C:K.92 T8W.5: 11 residues within 4Å: Chain C: K.9, K.10, T.13, K.16 Chain D: S.7, K.10, A.12, T.13, K.16 Ligands: T8W.4, 15P.8 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:K.10, D:K.10, D:A.12, D:T.13, D:K.16, C:T.13, C:K.16 Hydrogen bonds: D:S.7, C:S.7 Salt bridges: D:K.10, D:K.16, C:K.9, C:K.10, C:K.16 pi-Cation interactions: D:K.16, C:K.16 T8W.7: 8 residues within 4Å: Chain C: T.17, R.18, Q.21 Chain D: T.17, R.18, Q.21 Ligands: T8W.4, 15P.8 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.21, C:T.17 Hydrogen bonds: D:Q.21 Salt bridges: D:R.18, C:R.18 pi-Cation interactions: D:R.18, C:R.18

1 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.8: 4 residues within 4Å: Chain D: K.9 Ligands: T8W.4, T8W.5, T8W.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mockler, N.M. et al., Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with alpha-Helical Recognition Properties. Cryst.Growth Des. (2021)

Release Date

2021-10-20

Peptides

Cytochrome c iso-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytochrome c iso-1

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