SMTL ID : 8kcc.1

Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain K: Q.201, K.203, Q.206, M.229, G.230, L.231, G.232, K.233, T.234, I.235, R.271, N.608, R.636, I.637 Ligands: BEF.2 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:Q.201, K:Q.206, K:Q.206, K:M.229, K:K.233, K:T.234, K:T.234, K:R.271, K:R.271, K:N.608 Salt bridges: K:R.636, K:R.636 pi-Stacking: K:F.272 pi-Cation interactions: K:K.203

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 7 residues within 4Å: Chain K: T.261, D.333, E.334, G.606, R.633, R.636 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures. Structure (2024)

Release Date

2024-06-26

Peptides

Probable histone H2A.7: AB
Histone H2B.10: CD
Histone H3.1: EF
Histone H4: GH
ATP-dependent DNA helicase DDM1: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

K
K

Probable histone H2A.7

Histone H2B.10

Histone H3.1

Histone H4

ATP-dependent DNA helicase DDM1

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