9min

Structure of a designed minibinder to NYESO1-A*02:01

Method: X-RAY DIFFRACTION

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

HLA class I antigen

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1 × 1 （P78358） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 10 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1 × 1 （P78358） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53Z42_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–278； UniProt 24–300 Author chain F； PDBConstruct 2–278； UniProt 24–300

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	HLA class I antigen × 1 （Q53Z42） Cancer/testis antigen 1 × 1 （P78358） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 10 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	HLA class I antigen × 1 （Q53Z42） Cancer/testis antigen 1 × 1 （P78358） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–101； UniProt 21–119 Author chain G； PDBConstruct 3–101； UniProt 21–119

Cancer/testis antigen 1

OrganismNot specified

UniProt P78358

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	HLA class I antigen × 1 （Q53Z42） Beta-2-microglobulin × 1 （P61769） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 10 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	HLA class I antigen × 1 （Q53Z42） Beta-2-microglobulin × 1 （P61769） designed minibinder KH46 × 1 nanobody AD01 × 1 GLYCEROL × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTG1B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–9； UniProt 157–165 Author chain H； PDBConstruct 1–9； UniProt 157–165

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9min
Deposition date deposition_date	2024-12-13
Last revision last_revision	2025-08-06
Structure title title	Structure of a designed minibinder to NYESO1-A*02:01
Keywords keywords	complex, immune system, DE NOVO PROTEIN; DE NOVO PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

9min__assembly_1__model_1

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

Download this curve (.dat)

9min__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9min__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.05 Å
Rg (electron density)	28.37 Å
Total Rg	29.16 Å
Atom count	5115
Residues	629
Excluded volume	90486 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9min__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9min__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	HLA class I antigen
Molecular weight formula_weight	32139.6 kDa
Mutation mutation	insertion of MG at N-terminus - cloning artifact
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	10482

MGGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

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 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11936.4 kDa
Mutation mutation	insertion of MG at N-terminus - cloning artifact
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G

MGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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 3 Entity 3 polymer

Description description	Cancer/testis antigen 1
Molecular weight formula_weight	1090.3 kDa
Mutation mutation	C9V
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

SLLMWITQV

Entity 4 Entity 4 polymer

Description description	designed minibinder KH46
Molecular weight formula_weight	15361.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

MGAAERLQKMLEEAKELLKKSKEYLEKAKKLLKEGKVDEALKELEKALLYLVEAVNLLRVVSAELGDAELKALVEEAEKYLNKAVTYYYKAKLTKDPEEKKKYVEKSIEYAEKALKIAEEAVKLAEKVVAAAAALE

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	nanobody AD01
Molecular weight formula_weight	12762.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,J

EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSSGAP

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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Unit-cell length a length_a	95.452 Å
Unit-cell length b length_b	98.536 Å
Unit-cell length c length_c	155.743 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	49.270 Å
R factor r_factor	0.2550
R_work r_work	0.2548
R_free r_free	0.2673

Structure of a designed minibinder to NYESO1-A*02:01

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

HLA class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Cancer/testis antigen 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

9min__assembly_1__model_1

9min__assembly_1__model_1 | I(q)

9min__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structure of a designed minibinder to NYESO1-A*02:01

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

HLA class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cancer/testis antigen 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

9min__assembly_1__model_1

9min__assembly_1__model_1 | I(q)

9min__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)