5O45: Human PD-L1

Structure of human PD-L1 in complex with inhibitor. Determined by X-ray diffraction at 0.99 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 0.99 Å
Organisms: Homo sapiens, Synthetic construct
Chains: 2
Atoms: 1,657
Mol. weight: 16.61 kDa
Released: 20 Sept 2017

Explore 5O45 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O45 contains 4 α-helices and 10 β-strands across 1 chain. 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: 4 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	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	110-118	9	2
β-strand	120-131	12	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	129	Homo sapiens	Q9NZQ7 (AlphaFold model)
Phe-mea-9KK-sar-asp-val-mea-tyr-sar-trp-tyr-leu-ccs-gly-NH2	B	protein	15	Synthetic construct

Sequence of entity 1 (A), FASTA

>5O45_1 Programmed cell death 1 ligand 1 (chains A)
NAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKV
QHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAA
ALEHHHHHH

Sequence of entity 2 (B), FASTA

>5O45_2 PHE-MEA-9KK-SAR-ASP-VAL-MEA-TYR-SAR-TRP-TYR-LEU-CCS-GLY-NH2 (chains B)
FFXGDVFYGWYLCGX

Primary citation

Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Magiera-Mularz, K., Skalniak, L., Zak, K.M. et al. Angew Chem Int Ed Engl (2017) 56:13732-13735. DOI 10.1002/anie.201707707 · PubMed

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

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
5C3T 1.8 Å, PD-1 binding domain from human PD-L1

Browse structure collections

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