SMTL ID : 6e2b.1

Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.72, L.73, R.74, G.75 Chain B: K.6, G.10 11 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D, 4 interactions with chain A Water bridges: B:T.7, B:G.10, B:T.12, B:T.12, B:T.12, A:R.72 Salt bridges: B:K.6, D:K.11, A:R.72, A:R.74 Hydrogen bonds: A:G.75 SO4.2: 7 residues within 4Å: Chain A: R.42, Q.49, R.72, R.74 Chain B: K.6, T.66, H.68 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Water bridges: B:K.6, B:K.6, A:R.42, A:R.72 Salt bridges: B:K.6, B:H.68, A:R.42, A:R.72, A:R.74 Hydrogen bonds: A:Q.49 SO4.11: 8 residues within 4Å: Chain C: K.6, H.68 Chain D: K.6, H.68 Chain E: K.6, H.68 Ligands: GOL.10, GOL.12 14 PLIP interactions: 6 interactions with chain C, 6 interactions with chain E, 2 interactions with chain D Water bridges: C:K.6, C:K.6, C:K.6, C:H.68, E:K.6, E:K.6, E:K.6, E:K.6 Salt bridges: C:K.6, C:H.68, E:K.6, E:H.68, D:K.6, D:H.68 SO4.14: 6 residues within 4Å: Chain A: K.6, T.66, H.68 Chain F: R.42, Q.49, R.72 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain F Water bridges: A:K.6, A:K.6, A:T.66, F:Q.49, F:R.72, F:R.74, F:R.74 Salt bridges: A:K.6, A:H.68, F:R.42, F:R.72 Hydrogen bonds: F:Q.49 SO4.15: 3 residues within 4Å: Chain F: K.48, R.54, Y.59 3 PLIP interactions: 3 interactions with chain F Water bridges: F:R.54 Salt bridges: F:K.48, F:R.54 SO4.16: 7 residues within 4Å: Chain A: K.6, G.10 Chain E: K.11 Chain F: R.72, L.73, R.74, G.75 12 PLIP interactions: 4 interactions with chain F, 6 interactions with chain A, 2 interactions with chain E Hydrogen bonds: F:G.75 Water bridges: F:R.72, F:R.74, A:K.6, A:G.10, A:T.12, A:T.12, A:T.12, E:K.11 Salt bridges: F:R.72, A:K.6, E:K.11

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: F.45, S.65, T.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.65, A:T.66, A:T.66 Water bridges: A:Q.62 GOL.4: 3 residues within 4Å: Chain A: K.48, R.54, Y.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.54, A:R.54 GOL.6: 8 residues within 4Å: Chain B: R.42, Q.49, R.72 Chain C: K.11 Chain F: H.68 Ligands: GOL.7, GOL.9, PT7.17 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:H.68, B:R.42, B:Q.49, B:R.72 GOL.7: 9 residues within 4Å: Chain B: R.42, Q.49, E.51, R.72 Chain F: K.6, T.66, H.68 Ligands: GOL.6, GOL.9 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:T.66, B:R.42, B:E.51, B:R.72 Water bridges: F:K.6, F:K.6, B:R.72 GOL.9: 8 residues within 4Å: Chain B: R.72, R.74, G.75 Chain C: K.11 Chain F: K.6 Ligands: GOL.6, GOL.7, PT7.17 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.11, B:R.74, B:G.75 GOL.10: 10 residues within 4Å: Chain C: I.44, A.46, G.47, H.68 Chain D: A.46, G.47, H.68 Chain E: H.68 Ligands: SO4.11, GOL.12 8 PLIP interactions: 2 interactions with chain E, 3 interactions with chain C, 3 interactions with chain D Water bridges: E:A.46, E:H.68, D:G.47, D:G.47, D:G.47 Hydrogen bonds: C:A.46, C:G.47, C:H.68 GOL.12: 9 residues within 4Å: Chain C: T.66, H.68 Chain E: I.44, F.45, A.46, G.47, H.68 Ligands: GOL.10, SO4.11 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.47, C:T.66 Water bridges: E:A.46, E:H.68 GOL.13: 3 residues within 4Å: Chain E: K.48, R.54, Y.59 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.54, E:R.54 Water bridges: E:K.48, E:E.51, C:Q.62

3 x PT7: chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)platinum(2+)(Non-covalent)

PT7.5: 18 residues within 4Å: Chain A: K.6, T.7, L.8, I.44, A.46, G.47, H.68, L.69, V.70 Chain D: T.9 Chain E: T.9 Chain F: I.44, G.47, Q.49, V.70, R.72 Ligands: PT7.8, PT7.17 11 PLIP interactions: 5 interactions with chain A, 4 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: A:L.8, A:H.68, A:V.70, F:I.44, F:Q.49, F:V.70, E:T.9, D:T.9 pi-Stacking: A:H.68 Metal complexes: A:H.68 pi-Cation interactions: F:R.72 PT7.8: 18 residues within 4Å: Chain A: I.44, G.47, Q.49, V.70, R.72 Chain B: K.6, T.7, L.8, I.44, A.46, G.47, H.68, L.69, V.70 Chain C: T.9 Chain D: T.9 Ligands: PT7.5, PT7.17 11 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: C:T.9, A:I.44, A:Q.49, A:V.70, B:L.8, B:I.44, B:H.68, B:V.70 pi-Cation interactions: A:R.72 pi-Stacking: B:H.68 Metal complexes: B:H.68 PT7.17: 19 residues within 4Å: Chain B: I.44, G.47, Q.49, V.70 Chain C: T.9 Chain E: T.9 Chain F: K.6, T.7, L.8, I.44, A.46, G.47, H.68, L.69, V.70 Ligands: PT7.5, GOL.6, PT7.8, GOL.9 10 PLIP interactions: 6 interactions with chain F, 3 interactions with chain B, 1 interactions with chain E, Hydrophobic interactions: F:L.8, F:I.44, F:H.68, F:V.70, B:I.44, B:Q.49, B:V.70, E:T.9 pi-Stacking: F:H.68 Metal complexes: F:H.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Solomatina, A.I. et al., Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties via Ligand Design. Inorg Chem (2019)

Release Date

2018-11-14

Peptides

Ubiquitin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
I

F
P

Ubiquitin

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