5HQ8: Histone-lysine N-methyltransferase SMYD3

Name: PDB 5HQ8: Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A
Published: 2016-03-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A. Determined by X-ray diffraction at 1.72 Å resolution. Released 30 Mar 2016.

Method: X-ray diffraction
Resolution: 1.72 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,678
Mol. weight: 104.23 kDa
Ligands: SAH, MG, ZN
Released: 30 Mar 2016

Explore 5HQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HQ8 contains 49 α-helices and 38 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: 24 helices, 18 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
α-helix	42-44	3
β-strand	45	1	5
β-strand	48	1	5
β-strand	55	1	5
β-strand	60-61	2	6
β-strand	69-70	2	6
α-helix	73-93	21
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	264-268	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	410-427	18

Chain B: 25 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	73-93	21
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	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	1	8
α-helix	235	1
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	344-352	9
α-helix	355-361	7
α-helix	367-382	16
α-helix	386-403	18
α-helix	409-426	18

Chains I and J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	260	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SMYD3	A, B	protein	432	Homo sapiens	Q9H7B4 (AlphaFold model)
MEKK2 peptide	I, J	protein	16	Homo sapiens	Q9Y2U5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5HQ8_1 Histone-lysine N-methyltransferase SMYD3 (chains A, B)
GSFTMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGK
EKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGA
PSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFA
KVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELT
ICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEEL
KAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTME
PYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLIL
LLEECDANIRAS

Sequence of entity 2 (I, J), FASTA

>5HQ8_2 MEKK2 peptide (chains I, J)
YDNPIFEKFGKGGTYX

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	6

Water and common crystallization additives (GOL, EDO) are not listed.

Primary citation

Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets. Van Aller, G.S., Graves, A.P., Elkins, P.A. et al. Structure (2016) 24:774-781. DOI 10.1016/j.str.2016.03.010 · 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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