5gsu.1 | SWISS-MODEL Template Library

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SMTL ID : 5gsu.1

Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

CL.1:	7 residues within 4Å: Chain F: G.44, A.45, G.46, A.47 Chain H: S.91, S.92 Chain I: A.111 Ligand excluded by PLIP
CL.12:	2 residues within 4Å: Chain I: T.120 Ligands: MN.9 Ligand excluded by PLIP
CL.18:	2 residues within 4Å: Chain J: G.122, T.123 Ligand excluded by PLIP

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

MN.2:	3 residues within 4Å: Chain E: E.64 Chain G: V.49 Ligands: MN.3 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:V.49
MN.3:	3 residues within 4Å: Chain G: Q.48, V.49 Ligands: MN.2 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:V.49
MN.4:	2 residues within 4Å: Chain I: T.6, C.84 No protein-ligand interaction detected (PLIP)
MN.5:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.6:	3 residues within 4Å: Chain I: A.133, G.134 Ligands: MN.7 No protein-ligand interaction detected (PLIP)
MN.7:	2 residues within 4Å: Chain I: A.133 Ligands: MN.6 No protein-ligand interaction detected (PLIP)
MN.8:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.9:	3 residues within 4Å: Chain I: T.120, G.121 Ligands: CL.12 No protein-ligand interaction detected (PLIP)
MN.10:	2 residues within 4Å: Chain I: T.136, G.137 No protein-ligand interaction detected (PLIP)
MN.11:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.13:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.14:	2 residues within 4Å: Chain J: G.121, G.122 No protein-ligand interaction detected (PLIP)
MN.15:	2 residues within 4Å: Chain J: G.71, A.72 No protein-ligand interaction detected (PLIP)
MN.16:	1 residues within 4Å: Chain J: G.134 No protein-ligand interaction detected (PLIP)
MN.17:	2 residues within 4Å: Chain J: C.26, A.27 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Padavattan, S. et al., Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b. Biophys. Chem. (2017)

Release Date

2017-02-15

Peptides

Histone H3.1: AB
Histone H4: CD
Histone H2A type 1-A: EF
Histone H2B type 1-A: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
B

D
F

E
C

F
G

G
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

Toggle Identical (AB)

Histone H4

Histone H2A type 1-A

Histone H2B type 1-A

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