4ZQK: Programmed cell death 1 ligand 1

Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1. Determined by X-ray diffraction at 2.45 Å resolution. Released 4 Nov 2015.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,666
Mol. weight: 26.39 kDa
Released: 4 Nov 2015

Explore 4ZQK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZQK contains 6 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
β-strand	27-31	5	2
β-strand	36-41	6	1
α-helix	50-52	3
β-strand	54-59	6	2
β-strand	62-68	7	2
β-strand	71-72	2	2
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	1
α-helix	89-94	6
β-strand	96-101	6	1
α-helix	106-108	3
β-strand	110-117	8	2
β-strand	121-131	11	2

Chain B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	3
β-strand	41-45	5	4
β-strand	50-55	6	3
β-strand	62-70	9	4
β-strand	76-82	7	4
β-strand	95-99	5	3
β-strand	105-110	6	3
β-strand	119-129	11	4
β-strand	133-136	4	4
α-helix	137-139	3
β-strand	140-145	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	115	Homo sapiens	Q9NZQ7 (AlphaFold model)
Programmed cell death protein 1	B	protein	118	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ZQK_1 Programmed cell death 1 ligand 1 (chains A)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNA

Sequence of entity 2 (B), FASTA

>4ZQK_2 Programmed cell death protein 1 (chains B)
NPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQD
SRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAE

Primary citation

Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1. Zak, K.M., Kitel, R., Przetocka, S. et al. Structure (2015) 23:2341-2348. DOI 10.1016/j.str.2015.09.010 · PubMed

Other PDB entries of the same protein (UniProt Q9NZQ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5O45 0.99 Å, Structure of human PD-L1 in complex with inhibitor
8ALX 1.1 Å, Structure of human PD-L1 in complex with inhibitor
6NP9 1.27 Å, PD-L1 IgV domain V76T with fragment
9I0U 1.46 Å, Structure of human PD-L1 in complex with clinically evaluated inhibitor
6YCR 1.54 Å, Structure of human PD-L1 in complex with inhibitor
8AOK 1.6 Å, Complex of PD-L1 with VHH6
13DT 1.64 Å, Structure of FabS1CE2_P4a in complex with the N-terminal domain of PD-L1
7CZD 1.64 Å, Crystal structure of PD-L1 in complex with a VHH
5JDS 1.7 Å, Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution
5N2F 1.7 Å, Structure of PD-L1/small-molecule inhibitor complex
9QSM 1.75 Å, small molecule inhibitor in complex with PD-L1
8ZNL 1.77 Å, PD-L1 de novo designed binder with picomolar binding affinity

Browse structure collections

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