5y0d.1 | SWISS-MODEL Template Library

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SMTL ID : 5y0d.1

Crystal Structure of the human nucleosome containing the H2B E76K mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1:	3 residues within 4Å: Chain A: M.124, P.125, K.126 Ligand excluded by PLIP
CL.2:	6 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 Ligand excluded by PLIP
CL.3:	3 residues within 4Å: Chain E: M.124, P.125, K.126 Ligand excluded by PLIP
CL.5:	6 residues within 4Å: Chain G: G.48, A.49, G.50, A.51 Chain H: T.94, S.95 Ligand excluded by PLIP

10 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4:	1 residues within 4Å: Chain E: D.81 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.81, H₂O.6
MN.6:	1 residues within 4Å: Chain I: A.27 No protein-ligand interaction detected (PLIP)
MN.7:	1 residues within 4Å: Chain I: G.134 No protein-ligand interaction detected (PLIP)
MN.8:	1 residues within 4Å: Chain I: G.68 No protein-ligand interaction detected (PLIP)
MN.9:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.10:	1 residues within 4Å: Chain I: G.121 No protein-ligand interaction detected (PLIP)
MN.11:	1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP)
MN.12:	1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP)
MN.13:	3 residues within 4Å: Chain I: C.107 Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.14:	2 residues within 4Å: Chain J: G.71, A.72 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Arimura, Y. et al., Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res. (2018)

Release Date

2018-07-18

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

Histone H2B type 1-J

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