1PEG: Histone H3 methyltransferase DIM-5

Name: PDB 1PEG: Structural basis for the product specificity of histone lysine methyltransferases
Published: 2003-08-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structural basis for the product specificity of histone lysine methyltransferases. Determined by X-ray diffraction at 2.59 Å resolution. Released 5 Aug 2003.

Method: X-ray diffraction
Resolution: 2.59 Å
Organism: Neurospora crassa
Chains: 4
Atoms: 3,618
Mol. weight: 72.65 kDa
Ligands: SAH, ZN
Released: 5 Aug 2003

Explore 1PEG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PEG contains 13 α-helices and 46 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	1
β-strand	44-45	2	2
β-strand	50-51	2	3
β-strand	76	1	4
α-helix	80-82	3
β-strand	100	1	4
β-strand	104	1	5
β-strand	114	1	5
α-helix	116-121	6
α-helix	123-124	2
β-strand	125-126	2	6
α-helix	142-145	4
β-strand	151-155	5	1
β-strand	161-164	4	1
β-strand	169	1	7
β-strand	174-177	4	6
β-strand	181-183	3	3
α-helix	185-198	14
β-strand	205-207	3	3
β-strand	227-229	3	3
β-strand	233-234	2	2
α-helix	236-239	4
α-helix	240	1
β-strand	241-242	2	8
β-strand	248-254	7	6
β-strand	264-269	6	6
β-strand	273	1	7
β-strand	278-279	2	1
β-strand	280-281	2	8

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	28-31	4	9
β-strand	44-45	2	10
β-strand	50-51	2	11
β-strand	104	1	12
β-strand	114	1	12
α-helix	116-121	6
α-helix	123-124	2
β-strand	125-126	2	13
α-helix	142-145	4
β-strand	151-155	5	9
β-strand	161-164	4	9
β-strand	169	1	14
β-strand	174-178	5	13
β-strand	181-183	3	11
α-helix	185-196	12
β-strand	205-207	3	11
β-strand	227-229	3	11
β-strand	233-234	2	10
α-helix	236-239	4
α-helix	240	1
β-strand	241-242	2	15
β-strand	248-254	7	13
β-strand	264-269	6	13
β-strand	273	1	14
β-strand	278-279	2	9
β-strand	280-281	2	15
β-strand	305	1	16
β-strand	316	1	16

Chains P and Q: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
histone H3 methyltransferase DIM-5	A, B	protein	302	Neurospora crassa	Q8X225 (AlphaFold model)
Histone H3	P, Q	protein	15		P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1PEG_1 histone H3 methyltransferase DIM-5 (chains A, B)
IRSFATHAQLPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMY
STCQCLDEMAPDSDEEADPYTRKKRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSK
DCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAEST
IARRKDVYLFALDKFSDPDSLDPLLAGQPLEVDGEYMSGPTRFINHSCDPNMAIFARVGD
HADKHIHDLALFAIKDIPKGTELTFDYVNGLTGLESDAHDPSKISEMTKCLCGTAKCRGY
LW

Sequence of entity 2 (P, Q), FASTA

>1PEG_2 Histone H3 (chains P, Q)
ARTKQTARKSTGGKA

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2
ZN	Zinc ion	Zn	8

Primary citation

Structural basis for the product specificity of histone lysine methyltransferases. Zhang, X., Yang, Z., Khan, S.I. et al. Mol Cell (2003) 12:177-185. DOI 10.1016/S1097-2765(03)00224-7 · PubMed

Other PDB entries of the same protein (UniProt Q8X225 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ML9 1.98 Å, Structure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase

Browse structure collections

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