6PV9: Human PD-L1

Human PD-L1 bound to a macrocyclic peptide which blocks the PD-1/PD-L1 interaction. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,902
Mol. weight: 27.3 kDa
Released: 1 Jan 2020

Explore 6PV9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PV9 contains 6 α-helices and 24 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: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
β-strand	27-31	5	2
β-strand	36-38	3	3
β-strand	41	1	1
α-helix	50-52	3
β-strand	54-59	6	2
β-strand	62-68	7	2
β-strand	71	1	2
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	3
α-helix	89-92	4
β-strand	96	1	1
α-helix	98	1
β-strand	99-101	3	3
α-helix	106-108	3
β-strand	110-117	8	2
β-strand	121-131	11	2
β-strand	132	1	4
β-strand	138-145	8	5
β-strand	150-159	10	5
β-strand	160	1	4
β-strand	164-169	6	6
β-strand	174-175	2	6
β-strand	178-182	5	5
β-strand	191-200	10	5
β-strand	206-213	8	6
β-strand	218-225	8	6

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	7
β-strand	14-15	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	222	Homo sapiens	Q9NZQ7 (AlphaFold model)
macrocyclic peptide	B	protein	17	synthetic construct

Sequence of entity 1 (A), FASTA

>6PV9_1 Programmed cell death 1 ligand 1 (chains A)
MFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKI
NQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTL
RINTTTNEIFYCTFRRLDPEENHTAELVIPELPLAHPPNERT

Sequence of entity 2 (B), FASTA

>6PV9_2 macrocyclic peptide (chains B)
XFANPHLGWSWXXRCGX

Primary citation

Protein Footprinting and X-ray Crystallography Reveal the Interaction of PD-L1 and a Macrocyclic Peptide. Niu, B., Appleby, T.C., Wang, R. et al. Biochemistry (2020) 59:541-551. DOI 10.1021/acs.biochem.9b00822 · 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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