2NVU

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

Structural Biology Knowledgebase: 2NVU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NVU

Classification: PROTEIN TURNOVER LIGASE

Total Structure Weight: 188894.84

Macromolecule Entities
Molecule Chains Length Organism Details
NEDD8-activating enzyme E1 regulatory subunit A 536 Homo sapiens Gene Name(s): NAE1 Gene View APPBP1 HPP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera B 805 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: Residues 33-463
Details: Fusion protein. Maltose binding protein (residues 1001-1371), and the NEDD8-activating enzyme E1 catalytic subunit (residues 2012-2442) is from a human source
Gene Name(s): UBA3 Gene View UBE1C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NEDD8-conjugating enzyme Ubc12 C 180 Homo sapiens EC#: 6.3.2 IUBMB
Mutation: ΔS16, ΔA17, ΔG18, ΔG19, ΔT20, C111A
Gene Name(s): UBE2M Gene View UBC12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NEDD8 I, J 81 Homo sapiens Gene Name(s): NEDD8 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.241
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 156.49 α = 90.00
b = 156.49 β = 90.00
c = 190.49 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-13
  • Released Date: 2007-01-30
  • Deposition author(s): Huang, D.T., Hunt, H.W., Zhuang, M., Ohi, M.D., Holton, J.M., Schulman, B.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4