5UDZ Rna Binding Protein Rna date Dec 29, 2016
title Human Lin28a In Complex With Let-7f-1 Microrna Pre-Element
authors Y.Nam, L.Wang, P.Sliz
compound source
Molecule: Protein Lin-28 Homolog A
Chain: A, B
Fragment: Unp Residues 31-187
Synonym: Lin-28a,Zinc Finger Cchc Domain-Containing Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lin28a, Csdd1, Lin28, Zcchc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Let-7f-1 Pre-Element
Chain: V, W
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 41
R_factor 0.164 R_Free 0.200
length a length b length c angle alpha angle beta angle gamma
76.429 76.429 105.615 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ZN enzyme
A, B

Primary referenceLIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation., Wang L, Nam Y, Lee AK, Yu C, Roth K, Chen C, Ransey EM, Sliz P, Cell Rep. 2017 Mar 14;18(11):2664-2675. doi: 10.1016/j.celrep.2017.02.044. PMID:28297670
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (5udz.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (5udz.pdb2.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 5UDZ
  • CSU: Contacts of Structural Units for 5UDZ
  • Structure Factors (342 Kb)
  • Retrieve 5UDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UDZ from S2C, [Save to disk]
  • Re-refined 5udz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5UDZ 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 5UDZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5udz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5udz_V] [5udz_B] [5udz_W] [5udz_A] [5udz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5UDZ
  • Community annotation for 5UDZ at PDBWiki (http://pdbwiki.org)

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