4JDS: SETD7

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,940
Mol. weight: 122.16 kDa
Ligands: SAM, 1L4
Released: 27 Mar 2013

Explore 4JDS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JDS contains 32 α-helices and 80 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	1
β-strand	128-132	5	1
β-strand	141-147	7	1
β-strand	153-160	8	1
β-strand	163-176	14	1
β-strand	179-184	6	1
α-helix	185	1
β-strand	190-191	2	1
α-helix	210-215	6
β-strand	216-220	5	2
β-strand	228-232	5	2
β-strand	236	1	3
β-strand	241-245	5	4
β-strand	248-251	4	5
α-helix	252-257	6
α-helix	260-262	3
β-strand	267-268	2	5
β-strand	273-276	4	5
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	4
β-strand	303-310	8	4
β-strand	314-321	8	4
β-strand	325	1	3
α-helix	329	1
β-strand	330-331	2	2
β-strand	332-333	2	4
α-helix	351-363	13

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	6
β-strand	128-132	5	6
β-strand	141-147	7	6
β-strand	153-160	8	6
β-strand	163-176	14	6
β-strand	179-184	6	6
α-helix	185	1
β-strand	190-191	2	6
α-helix	210-213	4
β-strand	216-220	5	7
β-strand	228-232	5	7
β-strand	236	1	8
β-strand	241-245	5	9
β-strand	248-251	4	10
α-helix	252-257	6
α-helix	260-262	3
β-strand	267-268	2	10
β-strand	273-276	4	10
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	9
β-strand	303-310	8	9
β-strand	314-321	8	9
β-strand	325	1	8
α-helix	329	1
β-strand	330-331	2	7
β-strand	332-333	2	9
α-helix	351-363	13

Chain C: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	11
β-strand	128-132	5	11
β-strand	141-147	7	11
β-strand	153-160	8	11
β-strand	163-176	14	11
β-strand	179-184	6	11
α-helix	189-190	2
β-strand	191	1	11
α-helix	210-215	6
β-strand	216-220	5	12
β-strand	228-232	5	12
β-strand	236	1	13
β-strand	241-245	5	14
β-strand	248-250	3	15
α-helix	252-257	6
α-helix	260-262	3
β-strand	267-268	2	15
β-strand	274-276	3	15
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	14
β-strand	303-310	8	14
β-strand	314-321	8	14
β-strand	325	1	13
α-helix	329	1
β-strand	330-331	2	12
β-strand	332-333	2	14
α-helix	351-363	13
α-helix	367-369	3

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	16
β-strand	128-132	5	16
β-strand	141-147	7	16
β-strand	153-160	8	16
β-strand	163-176	14	16
β-strand	179-184	6	16
α-helix	185	1
β-strand	190-191	2	16
α-helix	210-213	4
β-strand	216-220	5	17
β-strand	228-232	5	17
β-strand	236	1	18
β-strand	241-245	5	19
β-strand	248-251	4	20
α-helix	252-257	6
β-strand	267-268	2	20
β-strand	273-276	4	20
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	19
β-strand	303-310	8	19
β-strand	314-321	8	19
β-strand	325	1	18
α-helix	329	1
β-strand	330-331	2	17
β-strand	332-333	2	19
α-helix	351-363	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD7	A, B, C, D	protein	264	Homo sapiens	Q8WTS6 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4JDS_1 Histone-lysine N-methyltransferase SETD7 (chains A, B, C, D)
QYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGK
LATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGE
GLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYC
ASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPE
APEWYQVELKAFQATQQKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	4
1L4	N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,…	C23 H25 F N4 O3 S	4

Water and common crystallization additives (UNX) are not listed.

Primary citation

SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine. Dong, A., Wu, H., Zeng, H. et al. To be published.

Other PDB entries of the same protein (UniProt Q8WTS6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F69 1.3 Å, Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide
3M58 1.4 Å, SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy
3CBP 1.42 Å, Set7/9-ER-Sinefungin complex
3M55 1.55 Å, SET7/9 Y305F in complex with TAF10-K189me1 peptide and AdoHcy
5EG2 1.55 Å, SET7/9 N265A in complex with AdoHcy and TAF10 peptide
4J7F 1.59 Å, SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy
3M54 1.6 Å, SET7/9 Y305F in complex with TAF10 peptide and AdoHcy
4J8O 1.63 Å, SET7/9 in complex with TAF10K189A peptide and AdoHcy
3CBO 1.65 Å, SET7/9-ER-AdoHcy complex
3M56 1.65 Å, SET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy
3CBM 1.69 Å, SET7/9-ER-AdoMet complex
3OS5 1.69 Å, SET7/9-Dnmt1 K142me1 complex

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