SMTL ID : 4rsz.7 (6 other biounits)

The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-hexamer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, K.79, M.80, I.81, L.94, L.98 Chain C: V.11 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:P.30, A:L.32, A:L.35, A:F.46, A:W.59, A:Y.67, A:L.68, A:M.80, A:L.94, A:L.98, C:V.11 Hydrogen bonds: A:G.41, A:T.49, A:N.52, A:T.78, A:T.78, A:K.79 Water bridges: A:R.38, A:A.43 Salt bridges: A:R.38, A:K.79 pi-Stacking: A:Y.67 Metal complexes: A:H.18 HEC.6: 27 residues within 4Å: Chain A: V.11 Chain B: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94, L.98 Ligands: NO3.5 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:F.46, B:W.59, B:Y.67, B:L.68, B:K.79, B:M.80, B:F.82, B:L.98, A:V.11 Hydrogen bonds: B:G.41, B:T.49, B:N.52, B:N.52, B:T.78, B:T.78, B:K.79 Water bridges: B:A.43 Salt bridges: B:R.38, B:K.79 pi-Stacking: B:Y.67 Metal complexes: B:H.18 HEC.10: 28 residues within 4Å: Chain C: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94, L.98 Ligands: NO3.8 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:L.32, C:L.32, C:L.35, C:F.46, C:W.59, C:Y.67, C:L.68, C:M.80, C:F.82, C:L.94, C:L.98 Hydrogen bonds: C:G.41, C:Q.42, C:T.49, C:N.52, C:N.52, C:T.78, C:T.78, C:K.79 Water bridges: C:R.38, C:A.43 Salt bridges: C:R.38, C:K.79 pi-Stacking: C:Y.67 Metal complexes: C:H.18 HEC.15: 26 residues within 4Å: Chain D: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94, L.98 Chain E: V.11 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: D:F.46, D:W.59, D:Y.67, D:L.68, D:M.80, D:F.82, D:L.94, D:L.98, E:V.11 Hydrogen bonds: D:G.41, D:Y.48, D:T.49, D:N.52, D:N.52, D:T.78, D:K.79 Water bridges: D:Q.42, D:A.43 Salt bridges: D:R.38, D:K.79 pi-Stacking: D:Y.67 Metal complexes: D:H.18 HEC.19: 28 residues within 4Å: Chain E: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, L.32, L.35, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94, L.98 Chain F: V.11 26 PLIP interactions: 25 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:L.32, E:L.32, E:L.35, E:F.46, E:W.59, E:Y.67, E:L.68, E:M.80, E:F.82, E:I.85, E:L.98, F:V.11 Hydrogen bonds: E:R.38, E:G.41, E:Q.42, E:Y.48, E:T.49, E:N.52, E:N.52, E:T.78, E:K.79 Water bridges: E:A.43, E:A.43 Salt bridges: E:K.79 pi-Stacking: E:Y.67 Metal complexes: E:H.18 HEC.25: 29 residues within 4Å: Chain D: V.11 Chain F: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94, L.98 26 PLIP interactions: 25 interactions with chain F, 1 interactions with chain D, Hydrophobic interactions: F:L.32, F:L.32, F:L.35, F:F.46, F:W.59, F:L.64, F:Y.67, F:L.68, F:K.79, F:M.80, F:F.82, F:L.98, D:V.11 Hydrogen bonds: F:G.41, F:Y.48, F:T.49, F:N.52, F:N.52, F:T.78, F:K.79 Water bridges: F:Q.42, F:A.43 Salt bridges: F:R.38, F:K.79 pi-Stacking: F:Y.67 Metal complexes: F:H.18

5 x CPT: Cisplatin(Non-covalent)(Covalent)

CPT.2: 1 residues within 4Å: Chain A: M.65 No protein-ligand interaction detected (PLIP) CPT.7: 5 residues within 4Å: Chain B: E.61, E.62, M.65, E.92 Chain D: E.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.61, B:E.61, B:E.62 CPT.12: 4 residues within 4Å: Chain C: E.61, M.65, K.88, E.92 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.92 Metal complexes: C:E.61 CPT.16: 3 residues within 4Å: Chain D: E.61, M.65, E.92 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.92, D:E.92, D:E.92 Metal complexes: D:E.61 CPT.21: 4 residues within 4Å: Chain E: E.61, E.62, M.65, E.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.62

16 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 7 residues within 4Å: Chain A: H.26, P.30, N.31, A.43, P.44, G.45, F.46 Ligand excluded by PLIP NO3.4: 7 residues within 4Å: Chain A: K.13, F.82, A.83, G.84 Chain C: K.8, V.11, Q.12 Ligand excluded by PLIP NO3.5: 8 residues within 4Å: Chain A: F.10, H.18, T.19, V.20, E.21 Chain B: T.28, I.81 Ligands: HEC.6 Ligand excluded by PLIP NO3.8: 7 residues within 4Å: Chain B: F.10, T.19, V.20, E.21 Chain C: T.28, I.81 Ligands: HEC.10 Ligand excluded by PLIP NO3.9: 6 residues within 4Å: Chain A: K.8, V.11, Q.12 Chain B: F.82, A.83, G.84 Ligand excluded by PLIP NO3.13: 7 residues within 4Å: Chain A: T.28, I.81 Chain C: F.10, H.18, T.19, V.20, E.21 Ligand excluded by PLIP NO3.14: 7 residues within 4Å: Chain B: K.7, K.8, V.11, Q.12 Chain C: F.82, A.83, G.84 Ligand excluded by PLIP NO3.17: 6 residues within 4Å: Chain D: F.10, T.19, V.20, E.21 Chain F: T.28, I.81 Ligand excluded by PLIP NO3.18: 6 residues within 4Å: Chain D: F.82, A.83, G.84 Chain E: K.8, V.11, Q.12 Ligand excluded by PLIP NO3.22: 7 residues within 4Å: Chain D: T.28, I.81 Chain E: F.10, H.18, T.19, V.20, E.21 Ligand excluded by PLIP NO3.23: 6 residues within 4Å: Chain E: F.82, A.83, G.84 Chain F: K.8, V.11, Q.12 Ligand excluded by PLIP NO3.24: 4 residues within 4Å: Chain E: G.41, F.46, T.47, Y.48 Ligand excluded by PLIP NO3.26: 7 residues within 4Å: Chain E: T.28, I.81 Chain F: F.10, H.18, T.19, V.20, E.21 Ligand excluded by PLIP NO3.27: 6 residues within 4Å: Chain D: K.8, V.11, Q.12 Chain F: F.82, A.83, G.84 Ligand excluded by PLIP NO3.28: 3 residues within 4Å: Chain E: A.83 Chain F: E.4, K.7 Ligand excluded by PLIP NO3.29: 3 residues within 4Å: Chain F: F.36, K.99, N.103 Ligand excluded by PLIP

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

SO4.11: 7 residues within 4Å: Chain A: K.25, K.27 Chain B: K.25, K.27 Chain C: Q.16, K.25, K.27 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:Q.16 Water bridges: C:K.27, A:K.27, A:T.28, B:K.25 Salt bridges: C:K.25, C:K.27, A:K.25, A:K.27, B:K.25, B:K.27 SO4.20: 3 residues within 4Å: Chain D: K.72 Chain E: K.100, E.104 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.104 Salt bridges: E:K.100, D:K.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, G. et al., The X-ray structure of the primary adducts formed in the reaction between cisplatin and cytochrome c. Chem.Commun.(Camb.) (2015)

Release Date

2015-01-14

Peptides

Cytochrome c: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
D

C
F

D
A

E
B

F
C

Cytochrome c

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