1R4N Cell Cycle date Oct 07, 2003
title Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex With
authors H.Walden, M.S.Podgorski, J.M.Holton, B.A.Schulman
compound source
Molecule: Amyloid Beta Precursor Protein-Binding Protein 1
Chain: A, C, E, G
Synonym: Appbp1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Activating Enzyme E1c
Chain: B, D, F, H
Synonym: Uba3
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Like Protein Nedd8
Chain: I, J, K, L
Synonym: Nedd8
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.251 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.000 197.900 211.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand ATP, ZN enzyme
note 1R4N (Molecule of the Month:pdb60)
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


J, K, I, L


Primary referenceThe structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1., Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL Jr, Holton JM, Schulman BA, Mol Cell 2003 Dec;12(6):1427-37. PMID:14690597
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (594 Kb) [Save to disk]
  • Biological Unit Coordinates (1r4n.pdb1.gz) 153 Kb
  • Biological Unit Coordinates (1r4n.pdb2.gz) 153 Kb
  • Biological Unit Coordinates (1r4n.pdb3.gz) 153 Kb
  • Biological Unit Coordinates (1r4n.pdb4.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 1R4N
  • CSU: Contacts of Structural Units for 1R4N
  • Likely Quarternary Molecular Structure file(s) for 1R4N
  • Retrieve 1R4N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R4N from S2C, [Save to disk]
  • View 1R4N in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1R4N
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1R4N, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r4na_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1r4nb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1r4nc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1r4nd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1r4ne_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1r4nf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1r4ng_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1r4nh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1r4ni_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1r4nj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1r4nk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1r4nl_, region L [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r4n_J] [1r4n_A] [1r4n_D] [1r4n_K] [1r4n_B] [1r4n] [1r4n_F] [1r4n_C] [1r4n_I] [1r4n_H] [1r4n_E] [1r4n_L] [1r4n_G]
  • SWISS-PROT database: [Q15843] [Q8TBC4] [Q13564]
  • Domain organization of [NEDD8_HUMAN] [UBA3_HUMAN] [ULA1_HUMAN] by SWISSPFAM
  • Domains found in 1R4N: [E2_bind] [UBQ ] by SMART
  • Other resources with information on 1R4N
  • Community annotation for 1R4N at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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