5xf5.1 | SWISS-MODEL Template Library

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SMTL ID : 5xf5.1

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1:

1 residues within 4Å:

Chain E: D.78

1 PLIP interactions:

1 interactions with chain E

Metal complexes: E:D.78

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

RUD.2:	6 residues within 4Å: Chain G: A.61, E.62, E.65, L.66 Chain H: V.49 Ligands: RSK.3 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.66 Salt bridges: G:E.62, G:E.65, G:E.65 Metal complexes: G:E.62, G:E.65
RUD.4:	3 residues within 4Å: Chain G: D.91, E.92 Ligands: RSK.3 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:E.92 Metal complexes: G:E.92

1 x RSK: (1S,2R)-1,2-diphenylethane-1,2-diamine(Non-covalent)

RSK.3:

3 residues within 4Å:

Chain G: D.91
Ligands: RUD.2, RUD.4

No protein-ligand interaction detected (PLIP)

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

SO4.5:

4 residues within 4Å:

Chain H: H.50, P.51, D.52, T.53

3 PLIP interactions:

3 interactions with chain H

Hydrogen bonds: H:D.52, H:T.53
Salt bridges: H:H.50

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 H3.1: AE
Histone H4: BF
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: 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 H3.1

Histone H4

Histone H2A type 1-B/E

Toggle Identical (CG)

Histone H2B type 1-J

Toggle Identical (DH)

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