Download MendeleyThe Crystal Structure of Core Jmjd2D
Chen, Z., Zhang, G.To be published.
3DXU
The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine
- PDB DOI: https://doi.org/10.2210/pdb3DXU/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-07-25 Released: 2009-07-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.221
- R-Value Work: 0.168
- R-Value Observed: 0.170
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| JmjC domain-containing histone demethylation protein 3D | 337 | Homo sapiens | Mutation(s): 0 Gene Names: JMJD2D, JHDM3D EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q6B0I6 (Homo sapiens) Explore Q6B0I6 Go to UniProtKB: Q6B0I6 | |||||
PHAROS: Q6B0I6 GTEx: ENSG00000186280 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6B0I6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OGA Query on OGA | G [auth A] | N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | D [auth A], E [auth A], F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | H [auth A], I [auth A], J [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| FE2 Query on FE2 | C [auth A] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.221
- R-Value Work: 0.168
- R-Value Observed: 0.170
- Space Group: P 43 21 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 71.543 | α = 90 |
| b = 71.543 | β = 90 |
| c = 150.194 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2009-07-28
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2018-07-04
Changes: Advisory, Data collection, Derived calculations - Version 1.3: 2019-12-11
Changes: Advisory, Database references, Derived calculations - Version 1.4: 2024-03-20
Changes: Advisory, Data collection, Database references, Derived calculations
