SAXSdb — 12np

▼

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

Secreted and transmembrane protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	T-cell antigen CD7 × 2 （P09564） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	T-cell antigen CD7 × 2 （P09564） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCTM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 29–137 Author chain B； PDBConstruct 1–109； UniProt 29–137 Author chain F； PDBConstruct 1–109； UniProt 29–137 Author chain H； PDBConstruct 1–109； UniProt 29–137

T-cell antigen CD7

Homo sapiens

UniProt P09564

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Secreted and transmembrane protein 1 × 2 （Q8WVN6） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Secreted and transmembrane protein 1 × 2 （Q8WVN6） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD7_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–120； UniProt 26–145 Author chain D； PDBConstruct 1–120； UniProt 26–145 Author chain E； PDBConstruct 1–120； UniProt 26–145 Author chain G； PDBConstruct 1–120； UniProt 26–145

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	12np
Deposition date deposition_date	2026-04-13
Last revision last_revision	2026-05-06
Structure title title	Crystal structure of the CD7 ectodomain bound to K12
Keywords keywords	Immunoglobulin, Immunoreceptor, surface receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

12np__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

12np__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

12np__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.74 Å
Rg (electron density)	24.92 Å
Total Rg	25.57 Å
Atom count	3444
Residues	446
Excluded volume	60049 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`12np__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`12np__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Secreted and transmembrane protein 1
Molecular weight formula_weight	11977.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,F,H
Atom count atom_count	7077

QNEGWDSPICTEGVVSVSWGENTVMSCNISNAFSHVNIKLRAHGQESAIFNEVAPGYFSRDGWQLQVQGGVAQLVIKGARDSHAGLYMWHLVGHQRNNRQVTLEVSGAE

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	T-cell antigen CD7
Molecular weight formula_weight	13162.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,E

AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDA

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

▶

Unit-cell length a length_a	49.681 Å
Unit-cell length b length_b	121.950 Å
Unit-cell length c length_c	88.871 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	44.990 Å
R factor r_factor	0.2431
R_work r_work	0.2414
R_free r_free	0.2781

Crystal structure of the CD7 ectodomain bound to K12

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

Secreted and transmembrane protein 1

State in the Current Structure

Other States of the Same Protein in the Database

T-cell antigen CD7

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

12np__assembly_2__model_1

12np__assembly_2__model_1 | I(q)

12np__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of the CD7 ectodomain bound to K12

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

Secreted and transmembrane protein 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

T-cell antigen CD7

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

12np__assembly_2__model_1

12np__assembly_2__model_1 | I(q)

12np__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)