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SMTL ID : 4kgc.1

Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x HRU: (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium(Non-covalent)(Non-functional Binders)

HRU.1:	7 residues within 4Å: Chain C: N.39, E.42 Chain G: N.39, A.41, E.42 Chain I: A.112, C.113 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:N.39, C:E.42, G:N.39, G:E.42
HRU.4:	3 residues within 4Å: Chain G: A.61, E.62, E.65 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.61 Hydrogen bonds: G:E.65 Metal complexes: G:E.65
HRU.7:	4 residues within 4Å: Chain I: G.58, G.59 Chain J: G.86, C.87 No protein-ligand interaction detected (PLIP)
HRU.8:	3 residues within 4Å: Chain I: C.87 Chain J: G.58, G.59 No protein-ligand interaction detected (PLIP)

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

SO4.2:	6 residues within 4Å: Chain C: A.46, G.47, A.48 Chain D: T.91, S.92 Chain J: T.111 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.47, C:A.48, D:S.92
SO4.5:	7 residues within 4Å: Chain G: G.45, A.46, G.47, A.48 Chain H: T.91, S.92 Chain I: T.111 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:A.46, G:G.47, G:A.48, H:S.92
SO4.6:	4 residues within 4Å: Chain H: H.50, P.51, D.52, T.53 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:H.50, H:D.52, H:D.52, H:T.53 Salt bridges: H:H.50

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

1 residues within 4Å:

Chain E: D.78

1 PLIP interactions:

1 interactions with chain E

Metal complexes: E:D.78

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Adhireksan, Z. et al., Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity. Nat Commun (2014)

Release Date

2014-03-26

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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