3RU0: SET and MYND domain-containing protein 3

Cocrystal structure of human SMYD3 with inhibitor Sinefungin bound. Determined by X-ray diffraction at 1.85 Å resolution. Released 18 May 2011.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,079
Mol. weight: 101.85 kDa
Ligands: ZN, SFG
Released: 18 May 2011

Explore 3RU0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RU0 contains 48 α-helices and 35 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: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	16-20	5	1
β-strand	24	1	2
β-strand	29-33	5	3
β-strand	37-40	4	4
β-strand	48	1	5
β-strand	55	1	5
β-strand	60-61	2	6
α-helix	62	1
β-strand	69-70	2	6
α-helix	73-83	11
α-helix	87-93	7
α-helix	100-111	12
α-helix	117-118	2
α-helix	119-121	3
α-helix	126-128	3
α-helix	133-135	3
α-helix	138-154	17
α-helix	162-164	3
α-helix	171-181	11
β-strand	183-186	4	4
β-strand	192-197	6	4
α-helix	201-203	3
α-helix	204	1
β-strand	205-206	2	7
β-strand	212-217	6	3
β-strand	220-225	6	3
β-strand	229	1	2
α-helix	233	1
β-strand	234-235	2	1
β-strand	236-237	2	7
α-helix	246-257	12
α-helix	264-267	4
α-helix	272-275	4
α-helix	280-298	19
α-helix	302-316	15
α-helix	325-340	16
α-helix	344-361	18
α-helix	367-382	16
α-helix	386-403	18
α-helix	409-427	19

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	16-20	5	8
β-strand	24	1	9
β-strand	29-33	5	10
β-strand	37-40	4	11
α-helix	42-44	3
β-strand	45	1	12
β-strand	48	1	12
β-strand	55	1	12
β-strand	60-61	2	13
β-strand	69-70	2	13
α-helix	73-83	11
α-helix	87-93	7
α-helix	100-111	12
α-helix	117-118	2
α-helix	119-121	3
α-helix	133-135	3
α-helix	138-154	17
α-helix	162-164	3
α-helix	171-181	11
β-strand	183-186	4	11
β-strand	192-197	6	11
α-helix	201-203	3
α-helix	204	1
β-strand	205-206	2	14
β-strand	212-217	6	10
β-strand	220-225	6	10
β-strand	229	1	9
α-helix	233	1
β-strand	234-235	2	8
β-strand	236-237	2	14
α-helix	246-257	12
α-helix	264-268	5
α-helix	272-275	4
α-helix	280-298	19
α-helix	302-315	14
α-helix	325-341	17
α-helix	344-353	10
α-helix	355-361	7
α-helix	367-382	16
α-helix	386-403	18
α-helix	409-421	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SET and MYND domain-containing protein 3	A, B	protein	438	Homo sapiens	Q9H7B4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3RU0_1 SET and MYND domain-containing protein 3 (chains A, B)
MALEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEK
LMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPS
ESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKV
ICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTIC
YLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKA
HWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPY
RIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLL
EECDANIRASEGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
SFG	Sinefungin	C15 H23 N7 O5	2

Primary citation

Structural and Functional Profiling of the Human Histone Methyltransferase SMYD3. Foreman, K.W., Brown, M., Park, F. et al. PLoS One (2011) 6:e22290-e22290. DOI 10.1371/journal.pone.0022290 · PubMed

Other PDB entries of the same protein (UniProt Q9H7B4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6P7Z 1.19 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
6PAF 1.24 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
5V37 1.42 Å, Crystal structure of SMYD3 with SAM and EPZ028862
5CCL 1.5 Å, Crystal structure of SMYD3 with SAM and oxindole compound
7O2C 1.52 Å, X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035
3QWP 1.53 Å, Crystal structure of SET and MYND domain containing 3; Zinc finger MYND…
6P6K 1.55 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
6ZRB 1.55 Å, Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127
7O2A 1.57 Å, X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH benzodiazepine-type inhibitor compound 15
7QNR 1.57 Å, SMYD3 in complex with fragment FL01791
6O9O 1.59 Å, Crystal Structure of SMYD3 with Potent and Selective Isoxazole Amide Inhibitor 1
6P6G 1.59 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

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