5xf6.1 | SWISS-MODEL Template Library

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SMTL ID : 5xf6.1

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

SO4.1:	6 residues within 4Å: Chain C: G.44, A.45, G.46, A.47 Chain D: T.90, S.91 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.46, C:A.47, D:S.91
SO4.3:	7 residues within 4Å: Chain G: G.44, A.45, G.46, A.47 Chain H: T.90, S.91 Chain I: A.110 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:A.45, G:G.46, G:A.47, H:S.91
SO4.6:	4 residues within 4Å: Chain H: H.49, P.50, D.51, T.52 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:D.51, H:D.51, H:D.51, H:T.52, H:T.52, H:T.52 Salt bridges: H:H.49

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

1 residues within 4Å:

Chain E: D.77

3 PLIP interactions:

1 interactions with chain E, 2 Ligand-Water interactions

Metal complexes: E:D.77, H₂O.1, H₂O.1

2 x RUD: [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2(Non-covalent)

RUD.4:	6 residues within 4Å: Chain G: A.60, E.61, E.64, L.65 Ligands: EDN.5, RUD.7 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:E.61, G:L.65 Salt bridges: G:E.61, G:E.64, G:E.64 Metal complexes: G:E.61, G:E.64
RUD.7:	4 residues within 4Å: Chain H: E.105, H.109 Ligands: RUD.4, EDN.5 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:E.105 Salt bridges: H:E.105, H:E.105 Metal complexes: H:E.105, H:H.109

1 x EDN: ETHANE-1,2-DIAMINE(Non-functional Binders)

EDN.5:

2 residues within 4Å:

Ligands: RUD.4, RUD.7

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Davey, G.E. et al., Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation. Nat Commun (2017)

Release Date

2017-10-11

Peptides

Histone H3.2: AE
Histone H4: BF
Histone H2A: CG
Histone H2B 1.1: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3.2

Toggle Identical (AE)

Histone H4

Histone H2A

Toggle Identical (CG)

Histone H2B 1.1

Toggle Identical (DH)

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