7DYV: Human JMJD5

Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid. Determined by X-ray diffraction at 1.92 Å resolution. Released 2 Feb 2022.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,179
Mol. weight: 27.59 kDa
Ligands: MN, HRF
Released: 2 Feb 2022

Explore 7DYV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DYV contains 14 α-helices and 19 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: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	183	1	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	1	1
α-helix	318-319	2
β-strand	321	1	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
Bifunctional peptidase and arginyl-hydroxylase JMJD5	A	protein	235	Homo sapiens	Q8N371 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7DYV_1 Bifunctional peptidase and arginyl-hydroxylase JMJD5 (chains A)
STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGS
RYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGE
EEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTS
QVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	1
HRF	5-(benzylamino)pyridine-2,4-dicarboxylic acid	C14 H12 N2 O4	1

Primary citation

5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5. Brewitz, L., Nakashima, Y., Piasecka, S.K. et al. J Med Chem (2023) 66:10849-10865. DOI 10.1021/acs.jmedchem.3c01114 · PubMed

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…
4QU1 1.57 Å, Crystal structure of human JMJD5 jmj-c domain

Browse structure collections

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