- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full PDF
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
4UXN|pdb_00004uxn
LSD1(KDM1A)-CoREST in complex with Z-Pro derivative of MC2580
- PDB DOI: https://doi.org/10.2210/pdb4UXN/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2014-08-27 Released: 2015-02-25
- Deposition Author(s): Rodriguez, V.,Valente, S.,Stazi, G.,Lucidi, A.,Mercurio, C.,Vianello, P.,Ciossani, G.,Mattevi, A.,Botrugno, O.A.,Dessanti, P.,Minucci, S.,Varasi, M.,Mai, A.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.215 (Depositor), 0.220 (DCC)
- R-Value Work: 0.206 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.206 (Depositor)
Starting Model:experimental
View more details
This is version 1.4 of the entry. See complete history.
Literature
Download MendeleyPyrrole- and Indole-Containing Tranylcypromine Derivatives as Novel Lysine-Specific Demethylase 1 Inhibitors Active on Cancer Cells
Rodriguez, V., Valente, S., Rovida, S., Rotili, D., Stazi, G., Lucidi, A., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Mercurio, C., Vianello, P., Minucci, S., Varasi, M., Mai, A.(2015) ChemMedChem 6: 665-670
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (FAD)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 147.28 kDa
- Atom Count: 6,374
- Modelled Residue Count: 799
- Deposited Residue Count: 1,334
- Unique protein chains: 2
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A | 852 | Homo sapiens | Mutation(s): 0 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60341 (Homo sapiens) Explore O60341 Go to UniProtKB: O60341 | |||||
PHAROS: O60341 GTEx: ENSG00000004487 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O60341 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| REST COREPRESSOR 1 | 482 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0 Go to UniProtKB: Q9UKL0 | |||||
PHAROS: Q9UKL0 GTEx: ENSG00000089902 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UKL0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD Query on FAD Download Ideal Coordinates CCD File | C [auth A] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | ||
| M8A Query on M8A Download Ideal Coordinates CCD File | D [auth A] | benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate C22 H24 N2 O4 ACUUWDZYZLDIFD-HXUWFJFHSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.215 (Depositor), 0.220 (DCC)
- R-Value Work: 0.206 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.206 (Depositor)
Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 118.98 | α = 90 |
| b = 177.76 | β = 90 |
| c = 233.72 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2015-02-25 Deposition Author(s): Rodriguez, V.,Valente, S.,Stazi, G.,Lucidi, A.,Mercurio, C.,Vianello, P.,Ciossani, G.,Mattevi, A.,Botrugno, O.A.,Dessanti, P.,Minucci, S.,Varasi, M.,Mai, A.
Revision History (Full details and data files)
- Version 1.0: 2015-02-25
Type: Initial release - Version 1.1: 2018-06-13
Changes: Data collection, Database references - Version 1.2: 2018-06-20
Changes: Advisory, Data collection, Derived calculations - Version 1.3: 2019-02-20
Changes: Advisory, Data collection, Derived calculations - Version 1.4: 2024-01-10
Changes: Data collection, Database references, Other, Refinement description
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.