4QU1: Human JMJD5 jmj-c domain

Crystal structure of human JMJD5 jmj-c domain. Determined by X-ray diffraction at 1.57 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,240
Mol. weight: 27.62 kDa
Ligands: AKG, NI
Released: 15 Jul 2015

Explore 4QU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QU1 contains 13 α-helices and 18 β-strands across 1 chain. 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: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	182-183	2	1
α-helix	184-185	2
β-strand	186-188	3	2
α-helix	192-195	4
α-helix	196-200	5
β-strand	206-209	4	2
α-helix	216-220	5
α-helix	223-230	8
β-strand	234-239	6	3
β-strand	249-254	6	3
α-helix	255-259	5
α-helix	260-264	5
β-strand	271-272	2	3
β-strand	273-276	4	2
α-helix	278-281	4
α-helix	283-286	4
α-helix	293-297	5
α-helix	302-304	3
β-strand	306-312	7	2
β-strand	317-321	5	1
β-strand	326-333	8	2
β-strand	336-341	6	1
α-helix	343-349	7
β-strand	351	1	4
β-strand	360	1	1
β-strand	361	1	4
α-helix	374-376	3
β-strand	382-386	5	1
β-strand	391-394	4	2
β-strand	399-404	6	1
β-strand	408-415	8	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific demethylase 8	A	protein	236	Homo sapiens	Q8N371 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4QU1_1 Lysine-specific demethylase 8 (chains A)
GSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVG
SRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDG
EEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNT
SQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS

Ligands and cofactors

ID	Name	Formula	Copies
AKG	2-oxoglutaric acid	C5 H6 O5	1
NI	Nickel (II) ion	Ni	1

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

Primary citation

The Histone Arginine Demethylase JMJD5. Liu, H.L., Wang, C., Dege, C. et al. To be published.

Other PDB entries of the same protein (UniProt Q8N371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4GJZ 1.05 Å, JMJD5 in complex with 2-oxoglutarate
6F4Q 1.12 Å, Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)
6F4T 1.22 Å, Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)
4GJY 1.25 Å, JMJD5 in complex with N-Oxalylglycine
6F4O 1.28 Å, Human JMJD5 in complex with Mn(II) and Succinate.
6F4R 1.3 Å, Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)
6I9N 1.36 Å, JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate
6F4P 1.45 Å, Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)
6F4S 1.46 Å, Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4)
7UQ3 1.49 Å, JmjC domain-containing protein 5 (JMJD5) in complex with Mn and…
6I9L 1.53 Å, JmjC domain-containing protein 5 (JMJD5) in complex with Mn and…
7DYT 1.62 Å, Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic…

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