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SMTL ID : 5ay8.1

Crystal structure of human nucleosome containing H3.Y

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

MN.1:	4 residues within 4Å: Chain A: R.67 Chain B: G.32, T.34, A.37 No protein-ligand interaction detected (PLIP)
MN.2:	6 residues within 4Å: Chain G: G.48, A.49, G.50, A.51 Chain H: T.94, S.95 No protein-ligand interaction detected (PLIP)
MN.3:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.4:	2 residues within 4Å: Chain I: G.15, C.16 No protein-ligand interaction detected (PLIP)
MN.5:	1 residues within 4Å: Chain J: G.137 No protein-ligand interaction detected (PLIP)
MN.6:	1 residues within 4Å: Chain J: G.137 No protein-ligand interaction detected (PLIP)
MN.7:	2 residues within 4Å: Chain J: A.133, G.134 No protein-ligand interaction detected (PLIP)
MN.8:	2 residues within 4Å: Chain I: G.46 Chain J: G.100 No protein-ligand interaction detected (PLIP)

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

CL.9:	1 residues within 4Å: Chain J: G.144 Ligand excluded by PLIP
CL.10:	1 residues within 4Å: Chain J: A.72 Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kujirai, T. et al., Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res. (2016)

Release Date

2016-04-06

Peptides

H3.Y: 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

H3.Y

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Toggle Identical (DH)

Related Entries With Identical Sequence

3a6n.1 | 3afa.1 | 3an2.1 | 3av1.1 | 3av2.1 | 3ayw.1 | 3aze.1 | 3azf.1 | 3azg.1 | 3azh.1 | 3azi.1 | 3azj.1 | 3azk.1 | 3azl.1 | 3azm.1 | 3azn.1 | 3w96.1 | 3w97.1 | 3w98.1 | 3w99.1 | 3wa9.1 | 3waa.1 | 3wkj.1 | 3wtp.1 | 4ym5.1 | 4ym6.1 | 4z5t.1 | 5av5.1 | 5av6.1 | 5av8.1 more...less...

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