8ZNL: PD-L1 de novo binder

PD-L1 de novo designed binder with picomolar binding affinity. Determined by X-ray diffraction at 1.77 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 1.77 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 8
Atoms: 6,059
Mol. weight: 80.76 kDa
Released: 4 Jun 2025

Explore 8ZNL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ZNL contains 32 α-helices and 43 β-strands across 8 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	24-41	18
α-helix	44-54	11

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	1
β-strand	28-31	4	2
β-strand	37-39	3	3
β-strand	42	1	1
α-helix	51-53	3
β-strand	55-60	6	2
β-strand	63-69	7	2
β-strand	72-73	2	2
α-helix	75-77	3
α-helix	80-82	3
β-strand	86-88	3	3
α-helix	90-95	6
β-strand	97	1	1
β-strand	100-102	3	3
α-helix	107-109	3
β-strand	111-118	8	2
β-strand	122-131	10	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-19	18
α-helix	24-41	18
α-helix	44-54	11

Chains D and F: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	4
β-strand	28-32	5	5
β-strand	37-42	6	4
α-helix	51-53	3
β-strand	55-60	6	5
β-strand	63-69	7	5
β-strand	72-73	2	5
α-helix	75-77	3
α-helix	80-82	3
β-strand	86-88	3	4
α-helix	90-95	6
β-strand	97-102	6	4
α-helix	107-109	3
β-strand	111-118	8	5
β-strand	122-132	11	5

Chains E and G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	24-41	18
α-helix	44-57	14

Chain H: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	8
β-strand	26	1	3
β-strand	28-32	5	9
β-strand	37-42	6	8
α-helix	51-53	3
β-strand	55-60	6	9
β-strand	63-69	7	9
β-strand	72-73	2	9
α-helix	75-77	3
α-helix	80-82	3
β-strand	86-88	3	8
α-helix	90-95	6
β-strand	97-102	6	8
α-helix	107-109	3
β-strand	111-118	8	9
β-strand	122-132	11	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PD-L1 de novo binder	A, C, E, G	protein	58	Escherichia coli
Programmed cell death 1 ligand 1	B, D, F, H	protein	114	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8ZNL_1 PD-L1 de novo binder (chains A, C, E, G)
GPDRERARELARILLKVIKLSDSPEARRQLLRNLEELAEKYKDPEVRRILEEAERYIK

Sequence of entity 2 (B, D, F, H), FASTA

>8ZNL_2 Programmed cell death 1 ligand 1 (chains B, D, F, H)
FTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQH
SSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNK

Primary citation

PD-L1 de novo binder. Zhao, L. To be published.

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

Browse structure collections

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