5GGS Immune System date Jun 16, 2016
title Pd-1 In Complex With Pembrolizumab Fab
authors Y.S.Heo
compound source
Molecule: Heavy Chain
Chain: A, C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Light Chain
Chain: B, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Programmed Cell Death Protein 1
Chain: Y, Z
Fragment: Unp Residues 26-148
Synonym: Hpd-1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd1, Pd1
Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4;
Expression_system_taxid: 1182032
symmetry Space Group: P 1
R_factor 0.180 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.170 54.195 104.039 105.69 96.99 96.06
method X-Ray Diffractionresolution 2.00 Å
Gene
Ontology
ChainFunctionProcessComponent
Z, Y


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (379 Kb) [Save to disk]
  • Biological Unit Coordinates (5ggs.pdb1.gz) 185 Kb
  • Biological Unit Coordinates (5ggs.pdb2.gz) 186 Kb
  • CSU: Contacts of Structural Units for 5GGS
  • Structure Factors (1796 Kb)
  • Retrieve 5GGS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GGS from S2C, [Save to disk]
  • Re-refined 5ggs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GGS 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 5GGS
  • 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
  • Fold representative 5ggs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ggs_C] [5ggs_A] [5ggs_Y] [5ggs_Z] [5ggs_D] [5ggs] [5ggs_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5GGS: [IG_like] [IGv ] by SMART
  • Other resources with information on 5GGS
  • Community annotation for 5GGS at PDBWiki (http://pdbwiki.org)

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