9Q8L: 21A08Ap1-Fab

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution. Determined by X-ray diffraction at 1.85 Å resolution. Released 13 Aug 2025.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,593
Mol. weight: 64.08 kDa
Ligands: NAG, PO4
Released: 13 Aug 2025

Explore 9Q8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q8L contains 24 α-helices and 56 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: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-38	3	12
β-strand	41-45	5	13
β-strand	50-55	6	12
β-strand	63-70	8	13
β-strand	76-82	7	13
β-strand	95-99	5	12
β-strand	105-110	6	12
α-helix	115-117	3
β-strand	119-127	9	13
β-strand	133-136	4	13
α-helix	137-139	3
β-strand	140-145	6	13
α-helix	146-147	2

Chain H: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	104-105	2	2
β-strand	109-113	5	2
α-helix	117-118	2
β-strand	119	1	3
α-helix	120-121	2
β-strand	122-126	5	4
α-helix	130-132	3
β-strand	133-134	2	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-156	4	5
α-helix	157-159	3
β-strand	161	1	5
β-strand	165-167	3	4
α-helix	168-170	3
β-strand	171-172	2	4
β-strand	178-187	10	4
α-helix	188-190	3
β-strand	197-202	6	5
α-helix	203-205	3
β-strand	207-212	6	5
α-helix	214-216	3

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
β-strand	9-12	4	7
β-strand	18-23	6	6
β-strand	35-39	5	7
β-strand	46-49	4	7
β-strand	50	1	8
β-strand	54	1	8
α-helix	55-56	2
β-strand	63-68	6	6
β-strand	71-76	6	6
α-helix	81-83	3
β-strand	85-93	9	7
β-strand	98-101	4	7
β-strand	105-109	5	7
α-helix	112-114	3
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-159	3	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-184	9	10
α-helix	186-191	6
β-strand	195-201	7	11
β-strand	204-210	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of huIgG1-Fab	H	protein	218	Mus musculus
Light chain of huIgG1-Fab	L	protein	216	Mus musculus
Programmed cell death protein 1	A	protein	147	Homo sapiens	Q15116 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9Q8L_1 Heavy chain of huIgG1-Fab (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSINAMTWVRQAPGKGLEWVSTISGSGFSTYY
ADSLKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKEVYGDYWGQGTLVTVSSASTKG
PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (L), FASTA

>9Q8L_2 Light chain of huIgG1-Fab (chains L)
RSVLTQPPSASGTPGQRVSISCSGASSNIGSQSVFWYQQLPGTAPKLLIYSNNQRPSGVP
DRFSGSKSGTSASLAISGLRSEDEADYYCAAWDDSLSIWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A), FASTA

>9Q8L_3 Programmed cell death protein 1 (chains A)
FLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFP
EDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELR
VTERRAEVPTAHPSPSPRPAGQFQTLV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (DMS, EDO) are not listed.

Primary citation

ANV600 is a novel PD-1 targeted IL-2R beta gamma agonist that selectively expands tumor antigen-specific T cells and potentiates PD-1 checkpoint inhibitor therapy. Murer, P., Petersen, L., Egli, N. et al. J Immunother Cancer (2025) 13. DOI 10.1136/jitc-2025-011905 · 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…
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

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