SMTL ID : 6ipu.1

Human nucleosome core particle containing 145 bp of DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-2-1-2-2-1-mer

Ligands

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

CL.1: 6 residues within 4Å: Chain C: G.32, A.33, G.34, A.35 Chain D: T.60, S.61 Ligand excluded by PLIP CL.3: 7 residues within 4Å: Chain G: G.32, A.33, G.34, A.35 Chain H: T.60, S.61 Chain I: T.111 Ligand excluded by PLIP

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

MN.2: 1 residues within 4Å: Chain D: V.18 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:V.18, H2O.2, H2O.2 MN.4: 1 residues within 4Å: Chain I: G.133 No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain I: A.101, G.102 No protein-ligand interaction detected (PLIP) MN.6: 1 residues within 4Å: Chain J: T.62 No protein-ligand interaction detected (PLIP) MN.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, D. et al., PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome. Nat Commun (2019)

Release Date

2020-01-15

Peptides

Histone H3.1: AE
Histone H4: B
Histone H2A type 1-B/E: CG
Histone H2B type 1-J: DH
Histone H4: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

C
C

G
G

D
D

H
H

F
F

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

Histone H4

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