6J14: Complex structure of GY-14 and PD-1

Complex structure of GY-14 and PD-1. Determined by X-ray diffraction at 1.4 Å resolution. Released 6 Nov 2019.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 2,958
Mol. weight: 38.46 kDa
Released: 6 Nov 2019

Explore 6J14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J14 contains 9 α-helices and 33 β-strands across 3 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	32-40	9	2
β-strand	44-52	9	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	65	1	1
β-strand	68-72	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	109-110	2	2
β-strand	114-118	5	2

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	3
β-strand	10-13	4	2
β-strand	19-25	7	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	3
β-strand	75-80	6	3
α-helix	85-87	3
β-strand	89-95	7	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2

Chain G: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	36-38	3	4
β-strand	41-45	5	5
β-strand	50-55	6	4
β-strand	65-70	6	5
β-strand	76-82	7	5
β-strand	95-99	5	4
β-strand	105-110	6	4
α-helix	115-117	3
β-strand	119-127	9	5
β-strand	133-136	4	5
α-helix	137-139	3
β-strand	140-145	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GY-14 heavy chain V fragment	A	protein	120	Mus musculus
GY-14 light chain V fragment	B	protein	112	Mus musculus
Programmed cell death protein 1	G	protein	115	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J14_1 GY-14 heavy chain V fragment (chains A)
QVQLQQSGAELVRPGASVKLSCKALGDTFTDYEIHWVKQTPVHGLEWIGVIHPGSGGTVY
NQKFKGKATLTADKYSSTAYMELSSLTSEDSAVYYCTREGMNTDWYFDVWGAGTTVTVSS

Sequence of entity 2 (B), FASTA

>6J14_2 GY-14 light chain V fragment (chains B)
DILMTQDELSLPVSLGDQASISCRSSQTIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTYFTLKISRLEAEDLGVYYCFQGSHVPYTFGGGTKLEMK

Sequence of entity 3 (G), FASTA

>6J14_3 Programmed cell death protein 1 (chains G)
NPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQD
CRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTER

Primary citation

The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy. Chen, D., Tan, S., Zhang, H. et al. iScience (2019) 14:113-124. DOI 10.1016/j.isci.2019.03.017 · PubMed

Other PDB entries of the same protein (UniProt Q15116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UMU 1.18 Å, Human apo PD-1 triple mutant
6UMV 1.42 Å, Human apo PD-1 double mutant
7WSL 1.53 Å, PD-1 in complex with Dostarlimab
9EHT 1.54 Å, Crystal Structure of PD-1/retifanlimab complex
7VUX 1.64 Å, Complex structure of PD1 and 609A-Fab
8EQ6 1.65 Å, PD1 signaling receptor bound to FAB Complex
6K0Y 1.7 Å, Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
7E9B 1.78 Å, Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody…
9Q8L 1.85 Å, Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution
8GY5 1.98 Å, High-resolution structure of the cemiplimab Fab in complex with PD-1
6UMT 1.99 Å, High-affinity human PD-1 PD-L2 complex
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

Browse structure collections

About this viewer

MolViewer shows 6J14 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.