5JDS: PD-L1

Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution. Determined by X-ray diffraction at 1.7 Å resolution. Released 12 Apr 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Camelidae, Homo sapiens
Chains: 2
Atoms: 2,057
Mol. weight: 30.36 kDa
Released: 12 Apr 2017

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

Secondary structure: helices and β-sheets

5JDS contains 9 α-helices and 21 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: 4 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	43-45	3
β-strand	54-59	6	4
β-strand	62-68	7	4
β-strand	71-72	2	4
α-helix	73-75	3
β-strand	85-87	3	3
α-helix	89-94	6
β-strand	96-101	6	3
α-helix	106-108	3
β-strand	110-118	9	4
β-strand	120-131	12	4

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	28-31	4
β-strand	33-39	7	2
β-strand	46-52	7	2
β-strand	58-60	3	2
β-strand	68-72	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	101-102	2
α-helix	105-108	4
α-helix	112-114	3
β-strand	117-118	2	2
β-strand	122-126	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody	B	protein	146	Camelidae
Programmed cell death 1 ligand 1	A	protein	124	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5JDS_1 Nanobody (chains B)
TGQVQLQESGGGLVQPGGSLRLSCAASGKMSSRRCMAWFRQAPGKERERVAKLLTTSGST
YLADSVKGRFTISQNNAKSTVYLQMNSLKPEDTAMYYCAADSFEDPTCTLVTSSGAFQYW
GQGTQVTVSSGSMDPGGSHHHHHHHH

Sequence of entity 2 (A), FASTA

>5JDS_2 Programmed cell death 1 ligand 1 (chains A)
MAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKV
QHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNALEHH
HHHH

Primary citation

Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade. Zhang, F., Wei, H., Wang, X. et al. Cell Discov (2017) 3:17004-17004. DOI 10.1038/celldisc.2017.4 · 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
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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