4JXT Protein Binding date Mar 28, 2013
title Cid Of Human Rprd1a In Complex With A Phosphorylated Peptide Rpb1-Ctd
authors Z.Ni, C.Xu, W.Tempel, M.El Bakkouri, P.Loppnau, X.Guo, C.Bountra, J C.H.Arrowsmith, A.M.Edwards, J.Min, J.F.Greenblatt, Structural Consortium (Sgc)
compound source
Molecule: Regulation Of Nuclear Pre-Mrna Domain-Containing 1a;
Chain: A
Fragment: Unp Residues 1-137
Synonym: Cyclin-Dependent Kinase Inhibitor 2b-Related Prote P15ink4b-Related Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rprd1a, P15rs
Expression_system_strain: Bl 21
Expression_system_plasmid: Pet15 Mhl

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: B
Fragment: Unp Residues 1612-1630
Synonym: Rna Polymerase II Subunit B1, Dna-Directed Rna Pol Subunit A, Dna-Directed Rna Polymerase III Largest Subunit, Directed Rna Polymerase II Subunit Rpb1;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: I 4
R_factor 0.184 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
93.264 93.264 36.027 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand SEP, UNX enzyme Transferase E.C. BRENDA

Primary referenceRPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation., Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WH, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF, Nat Struct Mol Biol. 2014 Jul 6. doi: 10.1038/nsmb.2853. PMID:24997600
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (4jxt.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 4JXT
  • CSU: Contacts of Structural Units for 4JXT
  • Structure Factors (970 Kb)
  • Retrieve 4JXT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JXT from S2C, [Save to disk]
  • Re-refined 4jxt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JXT 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 4JXT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4JXT, from MSDmotif at EBI
  • Fold representative 4jxt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jxt_A] [4jxt] [4jxt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JXT: [RPR ] by SMART
  • Other resources with information on 4JXT
  • Community annotation for 4JXT at PDBWiki (http://pdbwiki.org)

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