4GJY: JMJD5

JMJD5 in complex with N-Oxalylglycine. Determined by X-ray diffraction at 1.25 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,304
Mol. weight: 27.61 kDa
Ligands: OGA, CO
Released: 5 Sept 2012

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

Secondary structure: helices and β-sheets

4GJY 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	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	255-258	4
α-helix	259-263	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	343-348	6
β-strand	351	1	4
β-strand	360	1	1
β-strand	361	1	4
α-helix	374-378	5
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
JmjC domain-containing protein 5	A	protein	235	Homo sapiens	Q8N371 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4GJY_1 JmjC domain-containing protein 5 (chains A)
STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGS
RYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGE
EEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTS
QVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS

Ligands and cofactors

ID	Name	Formula	Copies
OGA	N-oxalylglycine	C4 H5 N O5	1
CO	Cobalt (II) ion	Co	1

Primary citation

Crystal Structure and Functional Analysis of JMJD5 Indicate an Alternate Specificity and Function. Del Rizzo, P.A., Krishnan, S., Trievel, R.C. Mol Cell Biol (2012) 32:4044-4052. DOI 10.1128/MCB.00513-12 · 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)
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
7DYT 1.62 Å, Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic…

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