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9q8l

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution

Method: X-RAY DIFFRACTION D_max: 95.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8l
deposition_date	2025-02-25
last_revision	2025-08-13
title	Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution
keywords	PD-1, Immune checkpoint, Fab, huIgG1, 21A08Ap1, T-cells, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	28.45 Å
rg_electron	27.85 Å
i0	60355400.00
molecular_weight	59568.0 kDa
excluded_volume	73983 Å³
envelope_volume	94042 Å³
shell_volume	29085 Å³
envelope_diameter	99.2 Å
shell_rg	34.27 Å
envelope_rg	27.83 Å
shape_rg	27.80 Å
total_rg	28.62 Å
total_atoms	4185
n_residues	545
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	95.3 Å
rg_real	28.58 Å
rg_real_error	0.66 Å
i0_real	6.0360e+07
i0_real_error	7.5680e+05
rg_reciprocal	28.54 Å
i0_reciprocal	60350000.0000
total_estimate	0.8762
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.437
kurtosis	-0.334
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	10470000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.896

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Heavy chain of huIgG1-Fab
formula_weight	23032.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	4593

EVQLLESGGGLVQPGGSLRLSCAASGFTFSINAMTWVRQAPGKGLEWVSTISGSGFSTYYADSLKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKEVYGDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 2 polymer

description	Light chain of huIgG1-Fab
formula_weight	22829.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

RSVLTQPPSASGTPGQRVSISCSGASSNIGSQSVFWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAAWDDSLSIWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Cricetulus griseus

Entity 3 polymer

description	Programmed cell death protein 1
formula_weight	16431.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

FLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	nat
entity_count	1

Entity 7 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	343

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6. Citations (1)

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length_a	61.839 Å
length_b	70.241 Å
length_c	163.684 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.850 Å
resolution_low	81.840 Å
r_factor	—
r_work	0.1778
r_free	0.2159

fit	/app/data/saxs_computation/q8/9q8l/9q8l.fit
pddf	/app/data/pr_computation/q8/9q8l/9q8l.pr.out
profile	/app/data/saxs_computation/q8/9q8l/9q8l.dat

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)