7CD9: SETDB1 tudor domain in

Crystal Structure of SETDB1 tudor domain in complexed with Compound 6. Determined by X-ray diffraction at 1.6 Å resolution. Released 7 Apr 2021.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,013
Mol. weight: 56.5 kDa
Ligands: CIT, FVR
Released: 7 Apr 2021

Explore 7CD9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CD9 contains 13 α-helices and 39 β-strands across 2 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	192	1	1
β-strand	194-195	2	2
β-strand	198-199	2	2
β-strand	203-207	5	1
β-strand	212	1	3
β-strand	213-224	12	1
β-strand	227-234	8	1
β-strand	239-242	4	1
α-helix	244-246	3
β-strand	247-249	3	1
α-helix	252-254	3
β-strand	263-270	8	3
β-strand	273-283	11	3
β-strand	293-297	5	3
β-strand	302-305	4	3
α-helix	307-309	3
β-strand	310-312	3	3
β-strand	313	1	1
α-helix	320-323	4
α-helix	327-339	13
β-strand	353-358	6	4
β-strand	361-371	11	4
β-strand	374-379	6	4
β-strand	385-389	5	4
β-strand	395	1	4
α-helix	396-404	9

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	194-195	2	5
β-strand	198-199	2	5
β-strand	203-207	5	6
β-strand	212	1	7
β-strand	213-224	12	6
β-strand	227-234	8	6
β-strand	239-243	5	6
α-helix	244-246	3
β-strand	247-249	3	6
α-helix	252-254	3
α-helix	255-257	3
β-strand	263-269	7	7
β-strand	274-283	10	7
β-strand	293-297	5	7
β-strand	302-305	4	7
α-helix	307-309	3
β-strand	310-312	3	7
β-strand	313	1	6
α-helix	320-323	4
α-helix	327-339	13
β-strand	353-358	6	8
β-strand	361-371	11	8
β-strand	374-379	6	8
β-strand	385-389	5	8
β-strand	395	1	8
α-helix	396-403	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETDB1	A, B	protein	240	Homo sapiens	Q15047 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7CD9_1 Histone-lysine N-methyltransferase SETDB1 (chains A, B)
GSSHHHHHHSSGENLYFQGGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKY
KVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNK
LRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKS
GQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALE

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2
FVR	3-methyl-2-[[(3R,5R)-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-5H…	C26 H29 N5 O2	2

Primary citation

Structure-Guided Discovery of a Potent and Selective Cell-Active Inhibitor of SETDB1 Tudor Domain. Guo, Y., Mao, X., Xiong, L. et al. Angew Chem Int Ed Engl (2021) 60:8760-8765. DOI 10.1002/anie.202017200 · PubMed

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
6AU2 1.63 Å, Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

Browse structure collections

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