5y0c.1 | SWISS-MODEL Template Library

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SMTL ID : 5y0c.1

Crystal Structure of the human nucleosome at 2.09 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

MN.1:	1 residues within 4Å: Chain A: A.27 No protein-ligand interaction detected (PLIP)
MN.2:	1 residues within 4Å: Chain A: G.134 No protein-ligand interaction detected (PLIP)
MN.3:	3 residues within 4Å: Chain A: G.68 Chain B: G.78, C.79 No protein-ligand interaction detected (PLIP)
MN.4:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.5:	1 residues within 4Å: Chain A: G.121 No protein-ligand interaction detected (PLIP)
MN.6:	2 residues within 4Å: Chain B: A.133, G.134 No protein-ligand interaction detected (PLIP)
MN.7:	1 residues within 4Å: Chain B: G.121 No protein-ligand interaction detected (PLIP)
MN.8:	2 residues within 4Å: Chain B: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.9:	1 residues within 4Å: Chain B: G.71 No protein-ligand interaction detected (PLIP)
MN.12:	1 residues within 4Å: Chain G: D.81 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.81, H₂O.10, H₂O.11

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

CL.10:	3 residues within 4Å: Chain C: M.124, P.125, K.126 Ligand excluded by PLIP
CL.11:	7 residues within 4Å: Chain B: T.112 Chain E: G.48, A.49, G.50, A.51 Chain F: T.94, S.95 Ligand excluded by PLIP
CL.13:	3 residues within 4Å: Chain G: M.124, P.125, K.126 Ligand excluded by PLIP
CL.14:	6 residues within 4Å: Chain I: G.48, A.49, G.50, A.51 Chain J: T.94, S.95 Ligand excluded by 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: CG
Histone H4: DH
Histone H2A type 1-B/E: EI
Histone H2B type 1-J: 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 type 1-B/E

Histone H2B type 1-J

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