5A7Q: Human JMJD2A

Crystal structure of human JMJD2A in complex with compound 30. Determined by X-ray diffraction at 2.0 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 6,044
Mol. weight: 89.63 kDa
Ligands: MN, KCH, ZN
Released: 13 Jan 2016

Explore 5A7Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A7Q contains 50 α-helices and 34 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
α-helix	13-14	2
β-strand	15-17	3	1
α-helix	21-25	5
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	1
α-helix	62-64	3
β-strand	66-67	2	2
β-strand	71-78	8	3
β-strand	81-88	8	3
β-strand	92-93	2	2
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	3
β-strand	133-137	5	1
α-helix	158-164	7
β-strand	175-179	5	1
β-strand	184-188	5	4
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	1
β-strand	206-211	6	4
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	3
α-helix	247-252	6
β-strand	258-262	5	4
α-helix	263	1
β-strand	267-270	4	1
β-strand	275-280	6	4
β-strand	284-291	8	1
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	326-328	3
α-helix	329-333	5
α-helix	345-347	3
α-helix	348-352	5

Chain B: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	14	1
β-strand	15-17	3	5
α-helix	21-25	5
α-helix	27-36	10
α-helix	39-42	4
β-strand	44-47	4	5
α-helix	48-50	3
β-strand	66-67	2	6
β-strand	71-78	8	7
β-strand	81-88	8	7
β-strand	92-93	2	6
α-helix	94-102	9
α-helix	108-110	3
α-helix	114-124	11
β-strand	131-132	2	7
β-strand	133-137	5	5
α-helix	150-152	3
α-helix	156-158	3
α-helix	159-164	6
β-strand	175-179	5	5
β-strand	184-188	5	8
α-helix	189-190	2
α-helix	191-193	3
β-strand	195-203	9	5
β-strand	206-211	6	8
α-helix	213-215	3
α-helix	216-226	11
α-helix	228-233	6
α-helix	237-240	4
β-strand	243-245	3	7
α-helix	247-252	6
β-strand	258-262	5	8
α-helix	263	1
β-strand	267-270	4	5
β-strand	275-280	6	8
β-strand	284-291	8	5
α-helix	296-302	7
α-helix	303-306	4
α-helix	318-324	7
α-helix	326-333	8
α-helix	345-347	3
α-helix	348-352	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 4A	A, B	protein	381	HOMO SAPIENS	O75164 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5A7Q_1 LYSINE-SPECIFIC DEMETHYLASE 4A (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQG
AHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFR
KIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKR
LERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAG
FNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDN
TVIDHTLPTPEAAEFLKESEL

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4
KCH	2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid	C12 H10 N2 O3	2
ZN	Zinc ion	Zn	2

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

Primary citation

Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. Korczynska, M., Le, D.D., Younger, N. et al. J Med Chem (2016) 59:1580. DOI 10.1021/ACS.JMEDCHEM.5B01527 · PubMed

Other PDB entries of the same protein (UniProt O75164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GP4 1.59 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
9GII 1.7 Å, Jumonji domain-containing protein 2A with crystallization epitope mutation R913A
6G5X 1.78 Å, Crystal Structure of KDM4A with compound YP-02-145
2QQR 1.8 Å, JMJD2A hybrid tudor domains
4V2W 1.81 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (16-35)
5VAR 1.83 Å, Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine…
6G5W 1.83 Å, Crystal Structure of KDM4A with compound YP-03-038
9GLE 1.88 Å, Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
2OX0 1.95 Å, Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9
6H8P 1.98 Å, JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
3PDQ 1.99 Å, Crystal structure of JMJD2A complexed with bipyridyl inhibitor
2P5B 1.99 Å, The complex structure of JMJD2A and trimethylated H3K36 peptide

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