5dnm.1 | SWISS-MODEL Template Library

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SMTL ID : 5dnm.1

Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

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

1 PLIP interactions:

1 interactions with chain E

Metal complexes: E:D.77

2 x RAX: dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium(Non-covalent)

RAX.4:	4 residues within 4Å: Chain G: A.60, E.61, E.64 Ligands: RAX.6 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Metal complexes: G:E.61, G:E.64 Salt bridges: H:E.113
RAX.6:	3 residues within 4Å: Chain H: E.105, H.109 Ligands: RAX.4 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Salt bridges: G:E.61 Metal complexes: H:H.109

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Adhireksan, Z. et al., Allosteric cross-talk in chromatin can mediate drug-drug synergy. Nat Commun (2017)

Release Date

2016-09-14

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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