6kvd.1 | SWISS-MODEL Template Library

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SMTL ID : 6kvd.1

Crystal structure of human nucleosome containing H2A.J

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

MN.1:	1 residues within 4Å: Chain A: G.121 No protein-ligand interaction detected (PLIP)
MN.2:	1 residues within 4Å: Chain A: G.134 No protein-ligand interaction detected (PLIP)
MN.3:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.4:	1 residues within 4Å: Chain A: G.68 No protein-ligand interaction detected (PLIP)
MN.5:	2 residues within 4Å: Chain A: C.26, A.27 No protein-ligand interaction detected (PLIP)
MN.6:	1 residues within 4Å: Chain A: G.100 No protein-ligand interaction detected (PLIP)
MN.7:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.8:	1 residues within 4Å: Chain B: G.121 No protein-ligand interaction detected (PLIP)
MN.9:	1 residues within 4Å: Chain B: G.71 No protein-ligand interaction detected (PLIP)
MN.10:	1 residues within 4Å: Chain B: G.134 No protein-ligand interaction detected (PLIP)
MN.11:	2 residues within 4Å: Chain B: A.57, G.58 No protein-ligand interaction detected (PLIP)
MN.12:	2 residues within 4Å: Chain B: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.14:	2 residues within 4Å: Chain E: E.68 Chain F: V.52 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:V.52, H₂O.6, H₂O.6, H₂O.7

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

CL.13:	3 residues within 4Å: Chain C: M.124, P.125, K.126 Ligand excluded by PLIP
CL.15:	6 residues within 4Å: Chain E: G.48, A.49, G.50, A.51 Chain F: T.94, S.95 Ligand excluded by PLIP
CL.16:	3 residues within 4Å: Chain G: M.124, P.125, K.126 Ligand excluded by PLIP
CL.17:	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

Tanaka, H. et al., Biochemical and structural analyses of the nucleosome containing human histone H2A.J. J.Biochem. (2020)

Release Date

2019-12-18

Peptides

Histone H3.1: CG
Histone H4: DH
Histone H2A.J: 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.J

Histone H2B type 1-J

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