SMTL ID : 7pr3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

4 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 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Q.21, A:V.33, A:I.40, A:Y.51, A:Y.72, A:L.73, A:L.73, A:M.85, A:F.87, A:L.99, A:L.99 Hydrogen bonds: A:G.46, A:Q.47, A:T.54, A:N.57, A:T.83, A:T.83, A:K.84 Water bridges: A:R.43 Salt bridges: A:K.84 Metal complexes: A:H.23 HEC.8: 27 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, Q.47, 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 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:V.33, B:L.37, B:L.37, B:I.40, B:Y.51, B:W.64, B:L.73, B:M.85, B:A.86, B:F.87 Hydrogen bonds: B:R.43, B:G.46, B:Q.47, B:Y.53, B:T.54, 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.19: 27 residues within 4Å: Chain C: R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Q.47, 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.90, L.99 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:V.33, C:L.37, C:I.40, C:Y.51, C:Y.53, C:L.73, C:M.85, C:A.86, C:F.87, C:L.90, C:L.99, C:L.99 Hydrogen bonds: C:G.46, C:Q.47, C:T.54, C:N.57, C:T.83, C:T.83, C:K.84 Water bridges: C:R.43, C:A.48 Salt bridges: C:K.84 pi-Stacking: C:Y.72 Metal complexes: C:H.23 HEC.35: 24 residues within 4Å: Chain D: R.18, C.19, 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 24 PLIP interactions: 24 interactions with chain D, Hydrophobic interactions: D:I.40, D:Y.51, D:Y.72, D:L.73, D:L.73, D:M.85, D:A.86, D:F.87, D:L.99, D:L.99 Hydrogen bonds: D:G.46, D:Q.47, D:Y.53, D:T.54, D:N.57, D:N.57, D:T.83, D:K.84 Water bridges: D:R.43, D:A.48, D:T.83 Salt bridges: D:K.84 pi-Stacking: D:Y.72 Metal complexes: D:H.23

33 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.2: 4 residues within 4Å: Ligands: 80M.3, ZN.34, ZN.46, PO4.47 No protein-ligand interaction detected (PLIP) ZN.5: 4 residues within 4Å: Chain A: K.27, H.38, T.107, E.108 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.38, A:E.108, A:E.108, H2O.1 ZN.6: 3 residues within 4Å: Ligands: 80M.4, ZN.28, PO4.32 No protein-ligand interaction detected (PLIP) ZN.7: 2 residues within 4Å: Chain A: E.2, E.93 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.2, A:E.93, A:E.93 ZN.9: 4 residues within 4Å: Ligands: 80M.10, ZN.16, ZN.18, PO4.30 No protein-ligand interaction detected (PLIP) ZN.12: 4 residues within 4Å: Chain B: K.27, H.38, T.107, E.108 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.38, B:E.108, B:E.108, H2O.2 ZN.13: 3 residues within 4Å: Chain B: E.2, E.93 Ligands: PO4.49 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.93 ZN.14: 4 residues within 4Å: Ligands: 80M.11, ZN.15, ZN.44, PO4.49 No protein-ligand interaction detected (PLIP) ZN.15: 5 residues within 4Å: Chain B: T.74 Ligands: 80M.11, ZN.14, ZN.45, PO4.49 No protein-ligand interaction detected (PLIP) ZN.16: 4 residues within 4Å: Ligands: ZN.9, 80M.10, ZN.17, PO4.30 No protein-ligand interaction detected (PLIP) ZN.17: 5 residues within 4Å: Chain C: H.44 Ligands: 80M.10, ZN.16, ZN.18, PO4.30 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.44, H2O.2 ZN.18: 4 residues within 4Å: Ligands: ZN.9, 80M.10, ZN.17, PO4.30 No protein-ligand interaction detected (PLIP) ZN.20: 4 residues within 4Å: Ligands: ZN.21, ZN.23, 80M.24, PO4.31 No protein-ligand interaction detected (PLIP) ZN.21: 4 residues within 4Å: Ligands: ZN.20, ZN.22, 80M.24, PO4.31 No protein-ligand interaction detected (PLIP) ZN.22: 4 residues within 4Å: Ligands: ZN.21, ZN.23, 80M.24, PO4.31 No protein-ligand interaction detected (PLIP) ZN.23: 4 residues within 4Å: Ligands: ZN.20, ZN.22, 80M.24, PO4.31 No protein-ligand interaction detected (PLIP) ZN.25: 4 residues within 4Å: Chain C: K.27, H.38, T.107, E.108 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.38, C:E.108, C:E.108, H2O.2, H2O.2 ZN.26: 3 residues within 4Å: Chain C: E.2, E.93 Ligands: PO4.32 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.2, C:E.93 ZN.27: 4 residues within 4Å: Chain C: E.71 Ligands: 80M.4, ZN.29, PO4.32 No protein-ligand interaction detected (PLIP) ZN.28: 4 residues within 4Å: Ligands: 80M.4, ZN.6, ZN.29, PO4.32 No protein-ligand interaction detected (PLIP) ZN.29: 5 residues within 4Å: Chain C: T.74 Ligands: 80M.4, ZN.27, ZN.28, PO4.32 No protein-ligand interaction detected (PLIP) ZN.33: 5 residues within 4Å: Chain D: H.44 Ligands: 80M.3, ZN.34, ZN.46, PO4.47 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.44, H2O.3 ZN.34: 4 residues within 4Å: Ligands: ZN.2, 80M.3, ZN.33, PO4.47 No protein-ligand interaction detected (PLIP) ZN.36: 4 residues within 4Å: Ligands: ZN.38, ZN.39, 80M.40, PO4.48 No protein-ligand interaction detected (PLIP) ZN.37: 4 residues within 4Å: Ligands: ZN.38, ZN.39, 80M.40, PO4.48 No protein-ligand interaction detected (PLIP) ZN.38: 4 residues within 4Å: Ligands: ZN.36, ZN.37, 80M.40, PO4.48 No protein-ligand interaction detected (PLIP) ZN.39: 4 residues within 4Å: Ligands: ZN.36, ZN.37, 80M.40, PO4.48 No protein-ligand interaction detected (PLIP) ZN.41: 4 residues within 4Å: Chain D: K.27, H.38, T.107, E.108 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.38, D:E.108, D:E.108, H2O.3 ZN.42: 2 residues within 4Å: Chain D: E.2, E.93 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.93, D:E.93 ZN.43: 1 residues within 4Å: Chain D: E.49 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.49, D:E.49 ZN.44: 3 residues within 4Å: Ligands: 80M.11, ZN.14, PO4.49 No protein-ligand interaction detected (PLIP) ZN.45: 3 residues within 4Å: Ligands: 80M.11, ZN.15, PO4.49 No protein-ligand interaction detected (PLIP) ZN.46: 4 residues within 4Å: Ligands: ZN.2, 80M.3, ZN.33, PO4.47 No protein-ligand interaction detected (PLIP)

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

80M.3: 15 residues within 4Å: Chain A: S.7, A.8, K.9, K.10, A.12 Chain D: H.44, N.61, V.62, L.63, N.68 Ligands: ZN.2, ZN.33, ZN.34, ZN.46, PO4.47 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:N.61, D:L.63, D:N.68, A:A.8, A:K.9 Water bridges: D:H.44 Hydrophobic interactions: A:K.9 Salt bridges: A:K.9, A:K.9, A:K.9 80M.4: 16 residues within 4Å: Chain A: E.71, T.74, N.75, K.78, K.91 Chain C: E.71, T.74, N.75, K.78, Y.79, K.91 Ligands: ZN.6, ZN.27, ZN.28, ZN.29, PO4.32 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:E.71, C:T.74, C:N.75, C:K.78 Hydrogen bonds: C:N.75, C:K.78, A:T.74, A:N.75 Salt bridges: C:K.78, C:K.91, A:K.78, A:K.91 80M.10: 14 residues within 4Å: Chain B: S.7, A.8, K.9, K.10 Chain C: H.44, N.61, V.62, L.63, N.68 Ligands: ZN.9, ZN.16, ZN.17, ZN.18, PO4.30 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:L.63 Hydrogen bonds: C:H.44, C:N.61, C:L.63, C:L.63, C:N.68, B:S.7, B:A.8, B:K.9 Salt bridges: B:K.9, B:K.9, B:K.10, B:K.16 80M.11: 14 residues within 4Å: Chain B: E.71, T.74, N.75, K.78, K.91 Chain D: E.71, T.74, N.75, K.78 Ligands: ZN.14, ZN.15, ZN.44, ZN.45, PO4.49 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:E.71, B:T.74 Hydrogen bonds: B:E.71, B:N.75, D:T.74, D:N.75 Salt bridges: B:K.78, B:K.78, B:K.91, D:K.78 Water bridges: D:K.78 80M.24: 9 residues within 4Å: Chain C: S.7, A.8, K.9, A.12 Ligands: ZN.20, ZN.21, ZN.22, ZN.23, PO4.31 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:K.9 Hydrogen bonds: C:S.7, C:K.9 Water bridges: C:K.9, C:K.9 Salt bridges: C:K.9, C:K.9 80M.40: 9 residues within 4Å: Chain D: S.7, A.8, K.9, A.12 Ligands: ZN.36, ZN.37, ZN.38, ZN.39, PO4.48 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.9 Hydrogen bonds: D:A.8, D:K.9 Salt bridges: D:K.9, D:K.9, D:K.10

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

PO4.30: 6 residues within 4Å: Chain C: H.44 Ligands: ZN.9, 80M.10, ZN.16, ZN.17, ZN.18 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.44 PO4.31: 5 residues within 4Å: Ligands: ZN.20, ZN.21, ZN.22, ZN.23, 80M.24 No protein-ligand interaction detected (PLIP) PO4.32: 9 residues within 4Å: Chain C: E.2, E.93, R.96 Ligands: 80M.4, ZN.6, ZN.26, ZN.27, ZN.28, ZN.29 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.96 PO4.47: 6 residues within 4Å: Chain D: H.44 Ligands: ZN.2, 80M.3, ZN.33, ZN.34, ZN.46 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.44 PO4.48: 5 residues within 4Å: Ligands: ZN.36, ZN.37, ZN.38, ZN.39, 80M.40 No protein-ligand interaction detected (PLIP) PO4.49: 9 residues within 4Å: Chain B: E.2, E.93, R.96 Ligands: 80M.11, ZN.13, ZN.14, ZN.15, ZN.44, ZN.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96

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: 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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