3BIK	Immune System	date	Nov 30, 2007
title	Crystal Structure Of The Pd-1pd-L1 Complex
authors	D.Y.Lin, Y.Tanaka, M.Iwasaki, A.G.Gittis, H.P.Su, B.Mikami, T.Okaz T.Honjo, N.Minato, D.N.Garboczi
compound		source
Molecule: Programmed Cell Death 1 Ligand 1 Chain: A Fragment: Extracellular Region Synonym: Programmed Death Ligand 1, Pd-L1, Pdcd1 Ligand 1, 1, B7-H1, Cd274 Antigen; 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 Expression_system_strain: Rosetta 2 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
Molecule: Programmed Cell Death Protein 1 Chain: B, C Fragment: Extracellular Domain Synonym: Protein Pd-1, Mpd-1, Cd279 Antigen Engineered: Yes Mutation: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Gene: Pdcd1, Pd1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta 2 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Plm1
symmetry	Space Group: P 21 21 21	R_factor 0.211 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.460 63.940 159.920 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	GOL	enzyme
Gene Ontology	Chain Function Process Component C, B
Primary reference	The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors., Lin DY, Tanaka Y, Iwasaki M, Gittis AG, Su HP, Mikami B, Okazaki T, Honjo T, Minato N, Garboczi DN, Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3011-6. Epub 2008 Feb 14. PMID:18287011

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk] Biological Unit Coordinates (3bik.pdb1.gz) 112 Kb Biological Unit Coordinates (3bik.pdb2.gz) 41 Kb LPC: Ligand-Protein Contacts for 3BIK CSU: Contacts of Structural Units for 3BIK Likely Quarternary Molecular Structure file(s) for 3BIK Structure Factors (141 Kb) Retrieve 3BIK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BIK from S2C, [Save to disk] Re-refined 3bik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BIK 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 3BIK

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3BIK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bik_A] [3bik_B] [3bik] [3bik_C] SWISS-PROT database: [Q9NZQ7] [Q02242] Domain organization of [PD1L1_HUMAN] [PDCD1_MOUSE] by SWISSPFAM Domains found in 3BIK: [IG] [IG_like ] by SMART

Other resources with information on 3BIK

Community annotation for 3BIK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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