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SMTL ID : 2cv5.1

Crystal structure of human nucleosome core particle

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

MN.1:	2 residues within 4Å: Chain A: G.68 Chain B: C.79 No protein-ligand interaction detected (PLIP)
MN.2:	1 residues within 4Å: Chain A: G.121 No protein-ligand interaction detected (PLIP)
MN.3:	1 residues within 4Å: Chain A: G.134 No protein-ligand interaction detected (PLIP)
MN.4:	2 residues within 4Å: Chain B: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.5:	2 residues within 4Å: Chain B: G.121, G.122 No protein-ligand interaction detected (PLIP)
MN.6:	1 residues within 4Å: Chain B: G.71 No protein-ligand interaction detected (PLIP)
MN.7:	2 residues within 4Å: Chain B: A.133, G.134 No protein-ligand interaction detected (PLIP)
MN.8:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.11:	2 residues within 4Å: Chain E: E.65 Chain F: V.49 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:V.49, H₂O.11

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

CL.9:	3 residues within 4Å: Chain C: M.121, P.122, K.123 Ligand excluded by PLIP
CL.10:	7 residues within 4Å: Chain B: T.112 Chain E: G.45, A.46, G.47, A.48 Chain F: T.91, S.92 Ligand excluded by PLIP
CL.12:	3 residues within 4Å: Chain G: M.121, P.122, K.123 Ligand excluded by PLIP
CL.13:	6 residues within 4Å: Chain I: G.45, A.46, G.47, A.48 Chain J: T.91, S.92 Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Tsunaka, Y. et al., Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucleic Acids Res. (2005)

Release Date

2005-06-28

Peptides

Histone H3.1: CG
Histone H4: DH
Histone H2A.a: EI
Histone H2B K: FJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

G
E

D
B

H
F

E
C

I
G

F
D

J
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.a

Histone H2B K

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1eqz.1 | 1f66.1 | 1hq3.1 | 1tzy.1 | 1u35.1 | 2aro.1 | 2f8n.1 | 3nqu.1 | 3r45.1 | 4hga.1 | 4kgc.1 | 4ld9.1 | 4z2m.1 | 4zux.1 | 4zux.2 | 5c3i.1 | 5c3i.2 | 5c3i.3 | 5c3i.4 | 5c3i.5 | 5c3i.6 | 5e5a.1 | 5kgf.1 | 5o9g.1 | 5omx.1 | 5ong.1 | 5onw.1 | 5x0x.1 | 5xf3.1 | 5xf4.1 more...less...

5xf5.1 | 6buz.1 | 6e0c.1 | 6e0p.1 | 6ftx.1 | 6g0l.1 | 6hts.1 | 6i84.1 | 6j99.1 | 6kw3.1 | 6kw4.1 | 6kw5.1 | 6l9z.1 | 6la2.1 | 6la8.1 | 6la9.1 | 6lab.1 | 6ler.1 | 6ler.2 | 6ltj.1 | 6m3v.1 | 6m44.1 | 6m4d.1 | 6m4g.1 | 6m4h.1 | 6ne3.1 | 6nzo.1 | 6o1d.1 | 6o22.1 | 6o96.1 | 6om3.1 | 6om3.2 | 6pa7.1 | 6pwv.1 | 6pww.1 | 6pwx.1 | 6px1.1 | 6px3.1 | 6r0c.1 | 6r8y.1 | 6rny.1 | 6ryr.1 | 6ryu.1 | 6se0.1 | 6se6.1 | 6see.1 | 6sef.1 | 6seg.1 | 6t79.1 | 6t7a.1 | 6t7b.1 | 6t7c.1 | 6t7d.1 | 6tem.1 | 6upk.1 | 6upl.1 | 6v92.1 | 6vz4.1 | 6w5i.1 | 6w5m.1 | 6w5n.1 | 6wkr.1 | 6y5d.1 | 6zhx.1 | 6zhy.1 | 7by0.1 | 7dbp.1 | 7jo9.1 | 7joa.1 | 7k5x.1 | 7k5y.1 | 7k60.1 | 7k61.1 | 7k63.1 | 7kbd.1 | 7kbe.1 | 7kbf.1 | 7m1x.1 | 7mbm.1 | 7mbn.1 | 7nkx.1 | 7nky.1 | 7nl0.1 | 7otq.1 | 7pet.1 | 7peu.1 | 7pev.1 | 7pew.1 | 7pex.1 | 7pey.1 | 7pez.1 | 7pf0.1 | 7pf2.1 | 7pf3.1 | 7pf4.1 | 7pf5.1 | 7pf6.1 | 7pfa.1 | 7pfc.1 | 7pfd.1 | 7pfe.1 | 7pff.1 | 7pft.1 | 7pfu.1 | 7pfv.1 | 7pfw.1 | 7pfx.1 | 7pii.1 | 7r5r.1 | 7ssa.1 | 7tan.1 | 7u0g.1 | 7u0i.1 | 7u0j.1 | 7u46.1 | 7u47.1 | 7u4d.1 | 7ud5.1 | 7unc.1 | 7und.1 | 7unk.1 | 7ux9.1 | 7v6q.1 | 7v6q.2 | 7v90.1 | 7v96.1 | 7v9c.1 | 7v9j.1 | 7v9k.1 | 7v9s.1 | 7va4.1 | 7vcq.1 | 7vcq.2 | 7vcq.3 | 7vdt.1 | 7vdv.1 | 7vvu.1 | 7vvz.1 | 7x3t.1 | 7x3v.1 | 7x3w.1 | 7x3x.1 | 7xfc.1 | 7xfh.1 | 7xfi.1 | 7xfj.1 | 7xfl.1 | 7xfm.1 | 7xfn.1 | 7xnp.1 | 7y5u.1 | 7y5v.1 | 7y5w.1 | 7y60.1 | 7y61.1 | 7y7i.1 | 7ywx.1 | 7yyh.1 | 7zi4.1 | 8aag.1 | 8b0a.1 | 8bvw.1 | 8byq.1 | 8bz1.1 | 8dk5.1 | 8du4.1 | 8ett.1 | 8etv.1 | 8eu2.1 | 8eue.1 | 8euj.1 | 8evg.1 | 8evh.1 | 8evi.1 | 8evj.1 | 8g6g.1 | 8g6h.1 | 8g6q.1 | 8g6s.1 | 8gpn.1 | 8gui.1 | 8guj.1 | 8guk.1 | 8gxq.12 | 8gxq.79 | 8gxs.12 | 8gxs.81 | 8h1t.1 | 8iqf.1 | 8iqg.1 | 8j6s.1 | 8j6t.1 | 8jh2.1 | 8jh3.1 | 8jh4.1 | 8jhf.1 | 8jhg.1 | 8of4.1 | 8off.1 | 8pki.1 | 8pkj.1 | 8rbx.1 | 8sps.1 | 8spu.1 | 8svf.1 | 8syp.1 | 8thu.1 | 8tof.1 | 8x15.1 | 8x19.1 | 8x1c.1 | 8yjf.1 | 8yjm.1 | 8yti.1

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