6UMT: High-affinity human PD-1 PD-L2 complex

High-affinity human PD-1 PD-L2 complex. Determined by X-ray diffraction at 1.99 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,769
Mol. weight: 29.4 kDa
Ligands: MG
Released: 27 Nov 2019

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

Secondary structure: helices and β-sheets

6UMT contains 5 α-helices and 18 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	36-38	3	1
β-strand	41-45	5	2
β-strand	50-55	6	1
β-strand	65-70	6	2
β-strand	76-82	7	2
β-strand	95-99	5	1
β-strand	105-110	6	1
α-helix	115-117	3
β-strand	119-127	9	2
β-strand	133-136	4	2
α-helix	137-139	3
β-strand	140-145	6	2
α-helix	146-148	3

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	3
β-strand	29-33	5	4
β-strand	38-45	8	3
β-strand	55-61	7	4
β-strand	74-75	2	3
α-helix	77-82	6
β-strand	84-89	6	3
α-helix	94-96	3
β-strand	98-106	9	4
β-strand	109-120	12	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death protein 1	A	protein	140	Homo sapiens	Q15116 (AlphaFold model)
Programmed cell death 1 ligand 2	B	protein	123	Homo sapiens	Q9BQ51 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UMT_1 Programmed cell death protein 1 (chains A)
MGWSCIILFLVATATGVHSNPPTFSPALLVVTEGDSATFTCSFSSTSESFVLNWYRMSPS
GQPDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRDDSGTYLCGAISLAPKVQ
IKESLRAELRVTERRAEPEA

Sequence of entity 2 (B), FASTA

>6UMT_2 Programmed cell death 1 ligand 2 (chains B)
MIFLLLMLSLELQLHQIAALFTVTVPKELYIIEHGSDVTLECNFDTGSHVNLGAITASLQ
KVEDDTSPHRERATLLEEQLPLGKASFHIPQVQVRDEGQYQCIIIYGVAWDYKYLTLKVK
ASY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery. Tang, S., Kim, P.S. Proc Natl Acad Sci U S A (2019) 116:24500-24506. DOI 10.1073/pnas.1916916116 · 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
6J14 1.4 Å, Complex structure of GY-14 and PD-1
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
5GGS 2.0 Å, PD-1 in complex with pembrolizumab Fab

Browse structure collections

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