3GZN

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924

Structural Biology Knowledgebase: 3GZN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GZN

Classification: PROTEIN BINDING / Ligase

Total Structure Weight: 244268.64

Macromolecule Entities
Molecule Chains Length Organism Details
NEDD8-activating enzyme E1 regulatory subunit A, C 534 Homo sapiens Gene Name(s): NAE1 Gene View APPBP1 HPP1
NEDD8-activating enzyme E1 catalytic subunit B, D 463 Homo sapiens EC#: 6.3.2 IUBMB
Gene Name(s): UBA3 Gene View UBE1C
NEDD8 I, J 82 Homo sapiens Gene Name(s): NEDD8 Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B39
Query on B39

I, J [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden- 1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}- 2-hydroxycyclopentyl]methyl sulfamate
C21 H25 N5 O4 S
MPUQHZXIXSTTDU-QXGSTGNESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
B39 N/A in BindingDB
N/A in BindingMoad
IC50: 10 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.230
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 135.03 α = 90.00
b = 228.71 β = 90.00
c = 229.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-07
  • Released Date: 2010-02-02
  • Deposition author(s): Sintchak, M.D.

Revision History

  • 2012-03-21
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4