5cp6.1 | SWISS-MODEL Template Library

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SMTL ID : 5cp6.1

Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

3 x RUH: (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl(Non-functional Binders)

RUH.1:	3 residues within 4Å: Chain A: A.57, G.58, G.59 No protein-ligand interaction detected (PLIP)
RUH.2:	4 residues within 4Å: Chain A: C.88 Chain B: A.57, G.58, G.59 No protein-ligand interaction detected (PLIP)
RUH.3:	4 residues within 4Å: Chain A: T.85, G.86 Chain B: T.62, G.63 No protein-ligand interaction detected (PLIP)

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

SO4.4:	7 residues within 4Å: Chain B: A.110 Chain E: G.44, A.45, G.46, A.47 Chain F: T.90, S.91 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.46, E:A.47, F:S.91
SO4.6:	7 residues within 4Å: Chain A: A.110 Chain I: G.44, A.45, G.46, A.47 Chain J: T.90, S.91 5 PLIP interactions: 1 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:S.91, I:G.44, I:A.45, I:G.46, I:A.47
SO4.7:	4 residues within 4Å: Chain J: H.49, P.50, D.51, T.52 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:D.51, J:T.52, J:T.52 Salt bridges: J:H.49

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5:

1 residues within 4Å:

Chain G: D.77

3 PLIP interactions:

1 interactions with chain G, 2 Ligand-Water interactions

Metal complexes: G:D.77, H₂O.1, H₂O.1

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ma, Z. et al., An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-06-01

Peptides

Histone H3.2: CG
Histone H4: DH
Histone H2A: EI
Histone H2B 1.1: FJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

G
E

D
B

H
F

E
C

I
G

F
D

J
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 (CG)

Histone H4

Histone H2A

Toggle Identical (EI)

Histone H2B 1.1

Toggle Identical (FJ)

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