5N2F Immune System date Feb 07, 2017
title Structure Of Pd-L1small-Molecule Inhibitor Complex
authors K.Guzik, K.M.Zak, P.Grudnik, G.Dubin, T.A.Holak
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A
Synonym: Programmed Death Ligand 1,B7 Homolog 1,B7-H1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd274, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Programmed Cell Death 1 Ligand 1
Chain: B
Synonym: Programmed Death Ligand 1,B7 Homolog 1,B7-H1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd274, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 2 21 21
R_factor 0.191 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.815 52.379 111.526 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand 8HW enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (5n2f.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 5N2F
  • CSU: Contacts of Structural Units for 5N2F
  • Structure Factors (1383 Kb)
  • Retrieve 5N2F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5N2F from S2C, [Save to disk]
  • Re-refined 5n2f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5N2F 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 5N2F
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5n2f_A] [5n2f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5N2F
  • Community annotation for 5N2F at PDBWiki (http://pdbwiki.org)

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