SAXSdb — 7dy7

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death 1 ligand 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-[[3-[[5-(2-methyl-3-phenyl-phenyl)-1,3,4-oxadiazol-2-yl]amino]phenyl]methylamino]ethanol × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PD1L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 18–134 Author chain B； PDBConstruct 1–117； UniProt 18–134

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7dy7
Deposition date deposition_date	2021-01-20
Structure title title	Discovery of Novel Small-molecule Inhibitors of PD-1/PD-L1 Axis that Promotes PD-L1 Internalization and Degradation
Keywords keywords	Immune checkpoint, Inhibitor, Complex, Dimer, IMMUNOSUPPRESSANT; IMMUNOSUPPRESSANT
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7dy7__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7dy7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dy7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.83 Å
Rg (electron density)	19.82 Å
Total Rg	20.69 Å
Atom count	2078
Residues	252
Excluded volume	36673 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dy7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Programmed cell death 1 ligand 1
Molecular weight formula_weight	14402.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	2082

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-[[3-[[5-(2-methyl-3-phenyl-phenyl)-1,3,4-oxadiazol-2-yl]amino]phenyl]methylamino]ethanol
Molecular weight formula_weight	400.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

▶

Unit-cell length a length_a	134.570 Å
Unit-cell length b length_b	32.682 Å
Unit-cell length c length_c	73.603 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.420 Å
Low-resolution limit resolution_low	23.472 Å
R factor r_factor	0.1982
R_work r_work	0.1964
R_free r_free	0.2396

Discovery of Novel Small-molecule Inhibitors of PD-1/PD-L1 Axis that Promotes PD-L1 Internalization and Degradation

1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death 1 ligand 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7dy7__assembly_1__model_1

7dy7__assembly_1__model_1 | I(q)

7dy7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Discovery of Novel Small-molecule Inhibitors of PD-1/PD-L1 Axis that Promotes PD-L1 Internalization and Degradation

1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death 1 ligand 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7dy7__assembly_1__model_1

7dy7__assembly_1__model_1 | I(q)

7dy7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)