7SJQ: Programmed cell death 1 ligand 1

Ex silico engineering of cystine-dense peptides yielding a potent bispecific T-cell engager. Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,289
Mol. weight: 19.64 kDa
Ligands: NAG
Released: 8 Jun 2022

Explore 7SJQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SJQ contains 7 α-helices and 10 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	53-59	7	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	85-88	4	1
α-helix	89-92	4
β-strand	96-101	6	1
α-helix	106-108	3
β-strand	110-118	9	2
β-strand	120-131	12	2

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
α-helix	41-49	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	119	Homo sapiens	Q9NZQ7 (AlphaFold model)
Cystine-dense peptide	D	protein	51	synthetic construct

Sequence of entity 1 (A), FASTA

>7SJQ_1 Programmed cell death 1 ligand 1 (chains A)
GSAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLK
VQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPY

Sequence of entity 2 (D), FASTA

>7SJQ_2 Cystine-dense peptide (chains D)
GSEEDCKVHCVKEWMAGKACAERQKSYTIGRAHCSGQKFDVFKCLDHCAAP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, SO4, NA) are not listed.

Primary citation

Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager. Crook, Z.R., Girard, E.J., Sevilla, G.P. et al. Sci Transl Med (2022) 14:eabn0402-eabn0402. DOI 10.1126/scitranslmed.abn0402 · 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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