3DLM: Histone-lysine N-methyltransferase SETDB1

Name: PDB 3DLM: Crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1
Published: 2008-08-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1. Determined by X-ray diffraction at 1.77 Å resolution. Released 12 Aug 2008.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,914
Mol. weight: 24.89 kDa
Released: 12 Aug 2008

Explore 3DLM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DLM contains 6 α-helices and 20 β-strands across 1 chain. 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	5-6	2	2
β-strand	9-10	2	2
β-strand	14-18	5	1
β-strand	23	1	3
β-strand	24-35	12	1
β-strand	38-45	8	1
β-strand	50-53	4	1
α-helix	55-57	3
β-strand	58-60	3	1
α-helix	63-65	3
α-helix	66-68	3
β-strand	74-80	7	3
β-strand	85-94	10	3
β-strand	104-108	5	3
β-strand	113-116	4	3
α-helix	118-120	3
β-strand	121-123	3	3
β-strand	124	1	1
α-helix	131-134	4
α-helix	138-150	13
β-strand	164-169	6	4
β-strand	172-182	11	4
β-strand	185-190	6	4
β-strand	195-200	6	4
β-strand	206	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETDB1	A	protein	213	Homo sapiens	Q15047 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DLM_1 Histone-lysine N-methyltransferase SETDB1 (chains A)
ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAY
DYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSE
LYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEE
VDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMK

Primary citation

The crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1. Dombrovski, L., Amaya, M.F., Loppnau, P. et al. To be published.

Other PDB entries of the same protein (UniProt Q15047 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
9CUX 1.27 Å, Crystal Structure of SETDB1 Tudor domain in complex with UNC100016
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHG 1.45 Å, Crystal structure of SETDB1 with a modified H3 peptide
5KCO 1.47 Å, SETDB1 in complex with an early stage, low affinity fragment candidate modelled at…
9CUW 1.53 Å, Crystal Structure of SETDB1 Tudor domain in complex with UNC100013
5KE2 1.56 Å, Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A
5QT1 1.58 Å, PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event…
5QT2 1.59 Å, PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event…
4X3S 1.6 Å, Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide
7CD9 1.6 Å, Crystal Structure of SETDB1 tudor domain in complexed with Compound 6

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