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SMTL ID : 3afa.1

The human nucleosome structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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:	7 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 Chain J: T.112 Ligand excluded by PLIP
CL.4:	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

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

MN.3:	1 residues within 4Å: Chain D: V.52 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:V.52, H₂O.3
MN.6:	1 residues within 4Å: Chain I: G.68 No protein-ligand interaction detected (PLIP)
MN.7:	3 residues within 4Å: Chain I: G.121, G.122 Chain J: C.25 No protein-ligand interaction detected (PLIP)
MN.8:	1 residues within 4Å: Chain I: A.133 No protein-ligand interaction detected (PLIP)
MN.9:	2 residues within 4Å: Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.10:	1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP)
MN.11:	1 residues within 4Å: Chain J: G.71 No protein-ligand interaction detected (PLIP)
MN.12:	1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Tachiwana, H. et al., Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-05-26

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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5avb.1 | 5avc.1 | 5ay8.1 | 5b0y.1 | 5b0z.1 | 5b1l.1 | 5b1m.1 | 5b24.1 | 5b2i.1 | 5b2j.1 | 5b31.1 | 5b32.1 | 5b33.1 | 5b40.1 | 5cpi.1 | 5cpj.1 | 5cpk.1 | 5gse.1 | 5gtc.1 | 5gxq.1 | 5jrg.1 | 5x7x.1 | 5xm0.1 | 5xm1.1 | 5y0c.1 | 5y0d.1 | 5z23.1 | 5z30.1 | 5zbx.1 | 6a5l.1 | 6a5o.1 | 6a5p.1 | 6a5r.1 | 6a5t.1 | 6a5u.1 | 6hkt.1 | 6inq.1 | 6ir9.1 | 6j4w.1 | 6j4x.1 | 6j4y.1 | 6j4z.1 | 6j50.1 | 6j51.1 | 6jou.1 | 6jr0.1 | 6jr1.1 | 6k1i.1 | 6k1j.1 | 6k1k.1 | 6kvd.1 | 6kxv.1 | 6l49.1 | 6l4a.1 | 6r8y.1 | 6r8z.1 | 6r90.1 | 6r91.1 | 6r92.1 | 6r93.1 | 6r94.1 | 6t90.1 | 6t93.1 | 6usj.1 | 6v2k.1 | 6yov.1 | 7bxt.1 | 7c0m.1 | 7d1z.1 | 7d20.1 | 7dbh.1 | 7scy.1 | 7scz.1 | 7vbm.1 | 7vz4.1 | 7w9v.1 | 7wbv.1 | 7wbw.1 | 7wbx.1 | 7x57.1 | 7x58.1 | 7xse.1 | 7xsx.1 | 7xsz.1 | 7xt7.1 | 7xtd.1 | 7xti.1 | 7xzx.1 | 7xzy.1 | 7xzz.1 | 7y00.1 | 7y7i.1 | 7yoz.1 | 8gui.1 | 8guj.1 | 8guk.1 | 8h0v.1 | 8h0w.1 | 8he5.1 | 8ihl.1 | 8jl9.1 | 8jlb.1 | 8jld.1 | 8jnd.1 | 8jne.1 | 8jnf.1 | 8kb5.1 | 8osj.1 | 8osk.1 | 8osl.1 | 8ots.1 | 8xbt.1 | 8xbu.1 | 8xbw.1 | 8ybj.1 | 8ybk.1

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