5b1l.1 | SWISS-MODEL Template Library

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SMTL ID : 5b1l.1

The mouse nucleosome structure containing H3t

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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:	6 residues within 4Å: Chain C: G.48, A.49, G.50, A.51 Chain D: T.94, S.95 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

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

MN.3:	1 residues within 4Å: Chain D: V.52 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:V.52, H₂O.2, H₂O.3, H₂O.3
MN.6:	1 residues within 4Å: Chain I: G.121 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 I: G.134 No protein-ligand interaction detected (PLIP)
MN.9:	2 residues within 4Å: Chain I: G.68 Chain J: C.79 No protein-ligand interaction detected (PLIP)
MN.10:	1 residues within 4Å: Chain I: T.86 No protein-ligand interaction detected (PLIP)
MN.11:	1 residues within 4Å: Chain I: A.17 No protein-ligand interaction detected (PLIP)
MN.12:	1 residues within 4Å: Chain J: G.121 No protein-ligand interaction detected (PLIP)
MN.13:	2 residues within 4Å: Chain J: G.39, G.40 No protein-ligand interaction detected (PLIP)
MN.14:	2 residues within 4Å: Chain J: A.133, G.134 No protein-ligand interaction detected (PLIP)
MN.15:	1 residues within 4Å: Chain J: T.37 No protein-ligand interaction detected (PLIP)
MN.16:	1 residues within 4Å: Chain J: G.71 No protein-ligand interaction detected (PLIP)
MN.17:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ueda, J. et al., Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis. Cell Rep (2017)

Release Date

2017-02-15

Peptides

Histone H3t: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B type 3-A: 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 H3t

Toggle Identical (AE)

Histone H4

Histone H2A type 1

Histone H2B type 3-A

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