5NIU: Programmed cell death 1 ligand 1

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor. Determined by X-ray diffraction at 2.01 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,349
Mol. weight: 60.03 kDa
Ligands: 8YZ
Released: 6 Dec 2017

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

Secondary structure: helices and β-sheets

5NIU contains 24 α-helices and 40 β-strands across 4 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	79-81	3
β-strand	85-87	3	1
α-helix	89-92	4
β-strand	96-101	6	1
α-helix	106-108	3
β-strand	110-117	8	2
β-strand	121-131	11	2
α-helix	134-142	9

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	27-31	5	4
β-strand	36-41	6	3
α-helix	50-52	3
β-strand	54-59	6	4
β-strand	62-68	7	4
β-strand	71-72	2	4
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	3
α-helix	89-92	4
β-strand	96-101	6	3
α-helix	106-108	3
β-strand	110-117	8	4
β-strand	121-131	11	4
α-helix	134-137	4

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	5
β-strand	27-31	5	6
β-strand	36-41	6	5
α-helix	48	1
α-helix	50-52	3
β-strand	54-59	6	6
β-strand	62-68	7	6
β-strand	71-72	2	6
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	5
α-helix	89-94	6
β-strand	96-101	6	5
α-helix	106-108	3
β-strand	110-117	8	6
β-strand	121-131	11	6
α-helix	134-140	7

Chain D: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	7
β-strand	27-31	5	8
β-strand	36-41	6	7
α-helix	50-52	3
β-strand	54-59	6	8
β-strand	62-68	7	8
β-strand	71-72	2	8
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	7
α-helix	89-94	6
β-strand	96-101	6	7
α-helix	106-108	3
β-strand	110-117	8	8
β-strand	121-131	11	8
α-helix	134-143	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A, B, C, D	protein	128	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5NIU_1 Programmed cell death 1 ligand 1 (chains A, B, C, D)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAA
LEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
8YZ	(2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)…	C35 H34 N2 O7	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells. Skalniak, L., Zak, K.M., Guzik, K. et al. Oncotarget (2017) 8:72167-72181. DOI 10.18632/oncotarget.20050 · 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

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