6NNV: Programmed cell death 1 ligand 1

PD-L1 IgV domain complex with macro-cyclic peptide. Determined by X-ray diffraction at 1.92 Å resolution. Released 20 Feb 2019.

Method: X-ray diffraction
Resolution: 1.92 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 4,561
Mol. weight: 65.58 kDa
Released: 20 Feb 2019

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

Secondary structure: helices and β-sheets

6NNV contains 15 α-helices and 40 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.

Chains A and D: 3 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
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	110-118	9	2
β-strand	120-131	12	2

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	27-31	5	4
β-strand	36-41	6	3
β-strand	54-59	6	4
β-strand	62-68	7	4
β-strand	71-72	2	4
α-helix	79-81	3
β-strand	85-87	3	3
α-helix	89-94	6
β-strand	96-101	6	3
α-helix	106-108	3
β-strand	110-118	9	4
β-strand	120-131	12	4
α-helix	135-138	4

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	5
β-strand	27-31	5	6
β-strand	36-41	6	5
α-helix	50-52	3
β-strand	54-59	6	6
β-strand	62-68	7	6
β-strand	72	1	6
α-helix	79-81	3
β-strand	85-87	3	5
α-helix	89-92	4
β-strand	96-101	6	5
α-helix	106-108	3
β-strand	110-118	9	6
β-strand	120-131	12	6
α-helix	135-141	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A, B, C, D	protein	127	Homo sapiens	Q9NZQ7 (AlphaFold model)
macrocyclic peptide	I, J, K, L	protein	16	synthetic construct

Sequence of entity 1 (A, B, C, D), FASTA

>6NNV_1 Programmed cell death 1 ligand 1 (chains A, B, C, D)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKTQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAA
LHEHHHH

Sequence of entity 2 (I, J, K, L), FASTA

>6NNV_2 macrocyclic peptide (chains I, J, K, L)
XFFXGDVFYGWYLCKX

Primary citation

Fragment-based screening of programmed death ligand 1 (PD-L1). Perry, E., Mills, J.J., Zhao, B. et al. Bioorg Med Chem Lett (2019) 29:786-790. DOI 10.1016/j.bmcl.2019.01.028 · 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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