SAXSdb — 3bdw

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

Natural killer cells antigen CD94

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 57–179	Fragment：Residues UNP 57-179	NKG2-A/NKG2-B type II integral membrane protein × 1 （P26715）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；1.0M tri-sodium citrate, 0.1M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.270
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 57–179	Fragment：Residues UNP 57-179	NKG2-A/NKG2-B type II integral membrane protein × 1 （P26715）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；1.0M tri-sodium citrate, 0.1M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.270

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3BDW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6E HUMAN CD94 Deposited 1999-01-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–179（128 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.60 Å R-free 0.322
3CDG Human CD94/NKG2A in complex with HLA-E Deposited 2008-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 57–179（123 aa） Fragment：residues in database 57-179	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291 K；Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.40 Å R-free 0.279
3CDG Human CD94/NKG2A in complex with HLA-E Deposited 2008-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 57–179（123 aa） Fragment：residues in database 57-179	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291 K；Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.40 Å R-free 0.279
3CII Structure of NKG2A/CD94 bound to HLA-E Deposited 2008-03-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 59–179（121 aa） Fragment：Ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.41 Å R-free 0.355
3CII Structure of NKG2A/CD94 bound to HLA-E Deposited 2008-03-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 59–179（121 aa） Fragment：Ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.41 Å R-free 0.355

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLRD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 57–179 Author chain C； PDBConstruct 1–123； UniProt 57–179

NKG2-A/NKG2-B type II integral membrane protein

Homo sapiens

UniProt P26715

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 113–232	Fragment：Residues UNP 113-232	Natural killer cells antigen CD94 × 1 （Q13241）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；1.0M tri-sodium citrate, 0.1M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.270
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 113–232	Fragment：Residues UNP 113-232	Natural killer cells antigen CD94 × 1 （Q13241）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；1.0M tri-sodium citrate, 0.1M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.270

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3BDW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RMX Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-11-30	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–15（15 aa） Fragment：tyrosine phosphorylation site, UNP residues 1-15	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YU7 Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–47（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.89mM SHP1 SH2 domain U-15N,13C; 0.89mM NKG2A peptide; 20mM d-Tris-HCl (pH 7.4); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CDG Human CD94/NKG2A in complex with HLA-E Deposited 2008-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 113–232（120 aa） Fragment：residues in database 113-232	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291 K；Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.40 Å R-free 0.279
3CDG Human CD94/NKG2A in complex with HLA-E Deposited 2008-02-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 113–232（120 aa） Fragment：residues in database 113-232	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；291 K；Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.40 Å R-free 0.279
3CII Structure of NKG2A/CD94 bound to HLA-E Deposited 2008-03-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 113–232（120 aa） Fragment：Ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.41 Å R-free 0.355
3CII Structure of NKG2A/CD94 bound to HLA-E Deposited 2008-03-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 113–232（120 aa） Fragment：Ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.41 Å R-free 0.355

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NKG2A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–120； UniProt 113–232 Author chain D； PDBConstruct 1–120； UniProt 113–232

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	3bdw
Deposition date deposition_date	2007-11-15
Structure title title	Human CD94/NKG2A
Keywords keywords	NK cells, receptor, Glycoprotein, Lectin, Membrane, Signal-anchor, Transmembrane, IMMUNE SYSTEM RECEPTOR; IMMUNE SYSTEM RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.19 Å
Radius of gyration Rg (electron density) rg_electron	29.87 Å
Forward intensity I(0) i0	54093800.00
Molecular weight molecular_weight	55214.0 kDa
Excluded volume excluded_volume	67945 Å³
Envelope volume envelope_volume	89326 Å³
Hydration-shell volume shell_volume	26615 Å³
Envelope diameter envelope_diameter	109.9 Å
Shell Rg shell_rg	34.30 Å
Envelope Rg envelope_rg	29.66 Å
Shape Rg shape_rg	29.91 Å
Total Rg total_rg	30.15 Å
Total atoms total_atoms	3871
Residues n_residues	477
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	104.0 Å
Rg (real space) rg_real	30.38 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	5.4090e+07
I(0) uncertainty (real space) i0_real_error	8.0240e+05
Rg (reciprocal space) rg_reciprocal	30.30 Å
I(0) (reciprocal space) i0_reciprocal	54090000.0000
Solution quality estimate total_estimate	0.8486
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.466
Kurtosis Kurtosis kurtosis	-0.242
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	11710000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.863

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Natural killer cells antigen CD94
Molecular weight formula_weight	14431.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3922

DCCSCQEKWVGYRCNCYFISSEQKTWNESRHLCASQKSSLLQLQNTDELDFMSSSQQFYWIGLSYSEEHTAWLWENGSALSQYLFPSFETFNTKNCIAYNPNGNALDESCEDKNRYICKQQLI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NKG2-A/NKG2-B type II integral membrane protein
Molecular weight formula_weight	13754.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ARHCGHCPEEWITYSNSCYYIGKERRTWEESLLACTSKNSSLLSIDNEEEMKFLSIISPSSWIGVFRNSSHHPWVTMNGLAFKHEIKDSDNAELNCAVLQVNRLKSAQCGSSIIYHCKHK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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	51

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3bdwa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3bdwb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3bdwc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d3bdwd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (4 domains)

Domain ID domain_id	3bdwA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3bdwB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3bdwC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	3bdwD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	44.651 Å
Unit-cell length b length_b	34.730 Å
Unit-cell length c length_c	152.896 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.590 Å
R factor r_factor	0.2360
R_work r_work	0.2340
R_free r_free	0.2700

fit	/app/data/saxs_computation/bd/3bdw/3bdw.fit
pddf	/app/data/pr_computation/bd/3bdw/3bdw.pr.out
profile	/app/data/saxs_computation/bd/3bdw/3bdw.dat

Human CD94/NKG2A

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

Natural killer cells antigen CD94

State in the Current Structure

Other States of the Same Protein in the Database

NKG2-A/NKG2-B type II integral membrane protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)