5NFN

JMJD7 IN COMPLEX WITH MN AND 2OG IN THE H32 FORM

PDB DOI: https://doi.org/10.2210/pdb5NFN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-14 Released: 2018-03-14
Deposition Author(s): Chowdhury, R., Markolovic, S., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.251
R-Value Work: 0.249
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

(3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7.

Markolovic, S., Zhuang, Q., Wilkins, S.E., Eaton, C., Katz, M.J., Smith, H.E., Lesniak, R.K., Hall, C., Struwe, W.B., Konietzny, R., Davis, S., Yang, M., Ge, W., Benesch, J.L., Kessler, B.M., Ratcliffe, P.J., Cockman, M.E., Fischer, R., Wappner, P., Chowdhury, R., Coleman, M.L., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 153.49 kDa
Atom Count: 10,336
Modelled Residue Count: 1,270
Deposited Residue Count: 1,340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JmjC domain-containing protein 7	A, B, C, D	335	Homo sapiens	Mutation(s): 0 Gene Names: JMJD7
UniProt & NIH Common Fund Data Resources
Find proteins for P0C870 (Homo sapiens) Explore P0C870 Go to UniProtKB: P0C870
GTEx: ENSG00000243789
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C870
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth D]	F [auth A], J [auth B], Q [auth D]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D]	K [auth B], L [auth B], M [auth B], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D]	G [auth A] H [auth A] O [auth C] S [auth D] T [auth D] G [auth A], H [auth A], O [auth C], S [auth D], T [auth D], U [auth D], V [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D]	E [auth A], I [auth B], N [auth C], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain P [auth D]