3mnn.1 | SWISS-MODEL Template Library

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SMTL ID : 3mnn.1

A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:A.45, C:G.46, C:A.47, D:S.91, D:S.91
SO4.6:	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: 3 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:A.45, G:G.46, G:A.47, H:S.91, H:S.91
SO4.10:	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

5 PLIP interactions:

1 interactions with chain E, 4 Ligand-Water interactions

Metal complexes: E:D.77, H₂O.1, H₂O.1, H₂O.1, H₂O.1

3 x RU: RUTHENIUM ION(Non-covalent)

RU.3:	4 residues within 4Å: Chain F: K.59, E.63 Ligands: MML.4, PTW.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.63
RU.7:	4 residues within 4Å: Chain G: E.61, E.64 Ligands: MML.8, PTW.9 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.61, G:E.64
RU.11:	3 residues within 4Å: Chain H: H.109 Ligands: MML.12, PTW.13 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.109

3 x MML: 1-methyl-4-(1-methylethyl)benzene(Non-covalent)

MML.4:	5 residues within 4Å: Chain E: F.78 Chain F: K.59, E.63 Ligands: RU.3, PTW.5 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:E.63, E:F.78
MML.8:	6 residues within 4Å: Chain G: E.61, E.64, L.65 Ligands: RU.7, PTW.9, PTW.13 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.64, G:L.65
MML.12:	5 residues within 4Å: Chain H: E.105, K.108, H.109 Ligands: RU.11, PTW.13 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:K.108

3 x PTW: 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane(Non-covalent)

PTW.5:	5 residues within 4Å: Chain F: K.59, V.60, E.63 Ligands: RU.3, MML.4 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:E.63, F:E.63
PTW.9:	5 residues within 4Å: Chain G: A.60, E.61, E.64 Ligands: RU.7, MML.8 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Salt bridges: G:E.61, G:E.64, G:E.64, H:E.113
PTW.13:	4 residues within 4Å: Chain H: H.109 Ligands: MML.8, RU.11, MML.12 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wu, B. et al., A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core. Chemistry (2011)

Release Date

2011-04-06

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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