8AOK: Complex of PD-L1 with VHH6

Complex of PD-L1 with VHH6. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Jun 2023.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, Lama glama
Chains: 2
Atoms: 2,305
Mol. weight: 28.13 kDa
Ligands: OXM
Released: 14 Jun 2023

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

Secondary structure: helices and β-sheets

8AOK contains 7 α-helices and 22 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
β-strand	27-30	4	2
β-strand	36-41	6	1
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	121-130	10	2

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	11-12	2	4
β-strand	18-25	8	3
β-strand	34-39	6	5
β-strand	46-51	6	5
β-strand	58-60	3	5
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-99	8	5
α-helix	103-106	4
α-helix	111-113	3
β-strand	114-117	4	5
β-strand	121-123	3	5
β-strand	124-125	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	117	Homo sapiens	Q9NZQ7 (AlphaFold model)
VHH 6	B	protein	128	Lama glama

Sequence of entity 1 (A), FASTA

>8AOK_1 Programmed cell death 1 ligand 1 (chains A)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKELDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPY

Sequence of entity 2 (B), FASTA

>8AOK_2 VHH 6 (chains B)
GEVQLVESGGGLVQAGGSLRLSCAASGRTFSNYHMAWFRQAPGKEREFVAGISWTGRGTY
YTDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAEGTLYGSGGRTHQSAYDYWGQ
GTQVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
OXM	Oxamic acid	C2 H3 N O3	1

Water and common crystallization additives (PEG, ACY, EDO, FMT, PG4) are not listed.

Primary citation

Identification, binding, and structural characterization of single domain anti-PD-L1 antibodies inhibitory of immune regulatory proteins PD-1 and CD80. Kang-Pettinger, T., Walker, K., Brown, R. et al. J Biol Chem (2023) 299:102769-102769. DOI 10.1016/j.jbc.2022.102769 · 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
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
5C3T 1.8 Å, PD-1 binding domain from human PD-L1

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