7CZD: PD-L1

Crystal structure of PD-L1 in complex with a VHH. Determined by X-ray diffraction at 1.64 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 1.64 Å
Organisms: Lama glama, Homo sapiens
Chains: 4
Atoms: 4,375
Mol. weight: 52.7 kDa
Released: 14 Jul 2021

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

Secondary structure: helices and β-sheets

7CZD contains 16 α-helices and 43 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: 3 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	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-97	6	2
β-strand	105	1	2
β-strand	109-113	5	2

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	27-31	5	2
β-strand	36-41	6	3
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	3
α-helix	89-92	4
β-strand	96-101	6	3
α-helix	106-108	3
β-strand	110-118	9	2
β-strand	120-131	12	2
α-helix	132-133	2

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	34-39	6	6
α-helix	44-45	2
β-strand	46-51	6	6
β-strand	58-60	3	6
α-helix	62-64	3
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-97	6	6
β-strand	105	1	6
β-strand	109-111	3	6
β-strand	112-113	2	5

Chain D: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	7
β-strand	27-31	5	6
β-strand	36-41	6	7
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	79-81	3
β-strand	85-87	3	7
α-helix	89-92	4
β-strand	96-101	6	7
α-helix	106-108	3
β-strand	110-118	9	6
β-strand	120-131	12	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-PD-L1 VHH	A, C	protein	116	Lama glama
Programmed cell death 1 ligand 1	B, D	protein	117	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7CZD_1 anti-PD-L1 VHH (chains A, C)
EVQLQESGGGLVQPGGSLRLSCAASGFTFSSYWMYWLRQAPGKGLEWVSSINSDSSSTYY
RDSVKGRFTISRDNAKNTLYLQMNSLKSEDTAVYYCAKDPGGYAKGQGTQVTVSSD

Sequence of entity 2 (B, D), FASTA

>7CZD_2 Programmed cell death 1 ligand 1 (chains B, D)
MFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPY

Primary citation

Generation of a safe and efficacious llama single-domain antibody fragment (vHH) targeting the membrane-proximal region of 4-1BB for engineering therapeutic bispecific antibodies for cancer. Zhai, T., Wang, C., Xu, Y. et al. J Immunother Cancer (2021) 9. DOI 10.1136/jitc-2020-002131 · 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
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

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