5NFN

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


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 1.2 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JmjC domain-containing protein 7
A, B, C, D
335Homo sapiensMutation(s): 0 
Gene Names: JMJD7
EC: 3.4 (UniProt), 1.14.11.63 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C870 (Homo sapiens)
Explore P0C870 
Go to UniProtKB:  P0C870
GTEx:  ENSG00000243789 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C870
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
Q [auth D]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B],
M [auth B],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
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
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
N [auth C],
P [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.240 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.22α = 90
b = 207.22β = 90
c = 211.788γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary