5ZWX: Raphanus sativus AGDP1 AGD12

Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Raphanus sativus, Arabidopsis thaliana
Chains: 4
Atoms: 2,814
Mol. weight: 40.45 kDa
Released: 14 Nov 2018

Explore 5ZWX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZWX contains 14 α-helices and 27 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	1
α-helix	46-48	3
β-strand	51-52	2	2
β-strand	53-59	7	1
β-strand	70-78	9	1
β-strand	86-91	6	1
α-helix	93-95	3
β-strand	96-97	2	1
α-helix	98-103	6
α-helix	105-109	5
α-helix	110-112	3
β-strand	117-122	6	2
β-strand	125-135	11	2
β-strand	139-144	6	2
β-strand	149-154	6	2
α-helix	155-157	3
β-strand	158-160	3	2
β-strand	163-165	3	3
β-strand	168-170	3	3

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	4
α-helix	46-48	3
β-strand	51-52	2	2
β-strand	53-59	7	4
β-strand	70-78	9	4
β-strand	86-91	6	4
α-helix	93-95	3
β-strand	96-97	2	4
α-helix	98-102	5
α-helix	106-109	4
α-helix	111-112	2
β-strand	117-122	6	2
β-strand	125-135	11	2
β-strand	139-144	6	2
β-strand	149-154	6	2
α-helix	155-157	3
β-strand	158-160	3	2
β-strand	163-165	3	5
β-strand	168-170	3	5

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4

Chain Q: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DUF724 domain-containing protein 6-like	A, B	protein	161	Raphanus sativus	A0A493R6M0 (AlphaFold model)
H3(1-15)K9me2 peptide	P, Q	protein	15	Arabidopsis thaliana	P59226 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5ZWX_1 DUF724 domain-containing protein 6-like (chains A, B)
SNSFAPRIRLPPFLKPGAAVEISSNESGFRGSWYMGKVVAVPSSDSTTTKCEVEYTTLFF
DKEGRKRLREVVDVGQLRPPAPAVSEREKRREVAVGDDVDAFYSDGWWEGTVTEVMGDGR
MSVYFRASKEQIRFRRDELRFHREWVNGAWRPPIEETEVDE

Sequence of entity 2 (P, Q), FASTA

>5ZWX_2 H3(1-15)K9me2 peptide (chains P, Q)
ARTKQTARKSTGGKA

Primary citation

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin. Zhang, C., Du, X., Tang, K. et al. Nat Commun (2018) 9:4547-4547. DOI 10.1038/s41467-018-06965-w · PubMed

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