1R4N

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

Structural Biology Knowledgebase: 1R4N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.251

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1R4N

Classification: CELL CYCLE

Total Structure Weight: 469486.56

Macromolecule Entities
Molecule Chains Length Organism Details
amyloid beta precursor protein-binding protein 1 A, C, E, G 529 Homo sapiens Mutation: ΔN254, ΔE255, ΔN256, ΔG257, ΔA258
Gene Name(s): NAE1 Gene View APPBP1 HPP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ubiquitin-activating enzyme E1C B, D, F, H 431 Homo sapiens EC#: 6.3.2 IUBMB
Mutation: C150A
Gene Name(s): UBA3 Gene View UBE1C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquitin-like protein NEDD8 I, J, K, L 76 Homo sapiens Gene Name(s): NEDD8 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

F, H, J ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.251
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 135.00 α = 90.00
b = 197.90 β = 90.00
c = 211.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-07
  • Released Date: 2003-12-23
  • Deposition author(s): Walden, H., Podgorski, M.S., Holton, J.M, Schulman, B.A.

Revision History

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