SAXSdb — 2eys

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

NKT15

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 42–226	Mutation：T164C	NKT15 × 1 （Q6GMR4） ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；297 K；9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.21 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 42–226	Mutation：T164C	NKT15 × 2 （Q6GMR4） ACY ACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；297 K；9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.21 Å R-free 0.278

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 2EYS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EYR A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 42–226（185 aa）	Mutation：T164C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；297 K；18% PEG 3350, 0.1M cacodylate, 0.2M lithium chloride, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.40 Å R-free 0.271
2EYR A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 42–226（185 aa）	Mutation：T164C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；297 K；18% PEG 3350, 0.1M cacodylate, 0.2M lithium chloride, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.40 Å R-free 0.271
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 42–226（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 42–226（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 42–226（185 aa） Chain C 42–226（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2F53 Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without apparent cross-reactivity Deposited 2005-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 42–210（169 aa）	Not recorded	NA SODIUM ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES, 8.5% Iso-propanol, 17% PEG4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.231
2F53 Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without apparent cross-reactivity Deposited 2005-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 42–210（169 aa）	Not recorded	NA SODIUM ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES, 8.5% Iso-propanol, 17% PEG4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.231
2F54 Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity Deposited 2005-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 42–224（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES, 8.5% iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.286
2F54 Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity Deposited 2005-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 42–224（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；85 mM HEPES, 8.5% iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.286
2P5W Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native diagonal binding geometry Deposited 2007-03-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 24–210（187 aa）	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 11 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；85 MM HEPES, 8.5% ISO-PROPANOL, 17% PEG4000, 15% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50	Resolution 2.20 Å R-free 0.245
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 122–223（102 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.293
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 122–223（102 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.293
2PYF Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry Unbound TCR Clone 5-1 Deposited 2007-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–215（191 aa）	Not recorded	SO4 SULFATE ION × 6 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；85 mM Na HEPES buffer pH7.5, 8.5 % iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.295

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PIZ8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–210； UniProt 42–226

NKT15

Homo sapiens

UniProt Q6GMR4

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 48–264	Mutation：S174C, C192A	NKT15 × 1 （Q6PIZ8） ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；297 K；9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.21 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 48–264	Mutation：S174C, C192A	NKT15 × 2 （Q6PIZ8） ACY ACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；297 K；9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.21 Å R-free 0.278

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 2EYS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AXJ Crystal structures of T cell receptor beta chains related to rheumatoid arthritis Deposited 2005-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–264（245 aa） Fragment：extracellular domain Chain B 20–264（245 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.6-0.7 M sodium citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.286
2AXJ Crystal structures of T cell receptor beta chains related to rheumatoid arthritis Deposited 2005-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 20–264（245 aa） Fragment：extracellular domain Chain B 20–264（245 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.6-0.7 M sodium citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.286
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 48–264（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 48–264（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2EYT A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Deposited 2005-11-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 48–264（217 aa） Chain D 48–264（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；0.2M sodium sulfate, 20% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.60 Å R-free 0.256
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 48–264（217 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.293
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 48–264（217 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.293

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6GMR4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 27–243； UniProt 48–264

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	2eys
Deposition date deposition_date	2005-11-09
Structure title title	A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition
Keywords keywords	Natural killer T cell receptor, NKT cell receptor, NKT15, IMMUNE SYSTEM; IMMUNE SYSTEM
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	25.24 Å
Radius of gyration Rg (electron density) rg_electron	24.21 Å
Forward intensity I(0) i0	45137100.00
Molecular weight molecular_weight	50223.0 kDa
Excluded volume excluded_volume	61988 Å³
Envelope volume envelope_volume	77204 Å³
Hydration-shell volume shell_volume	26528 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	31.46 Å
Envelope Rg envelope_rg	23.98 Å
Shape Rg shape_rg	24.21 Å
Total Rg total_rg	25.02 Å
Total atoms total_atoms	3535
Residues n_residues	445
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	75.7 Å
Rg (real space) rg_real	25.16 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	4.5140e+07
I(0) uncertainty (real space) i0_real_error	5.9770e+05
Rg (reciprocal space) rg_reciprocal	25.19 Å
I(0) (reciprocal space) i0_reciprocal	45140000.0000
Solution quality estimate total_estimate	0.9181
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.634
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11660000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NKT15
Molecular weight formula_weight	23365.8 kDa
Mutation mutation	T164C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3658

HMKNQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	NKT15
Molecular weight formula_weight	27701.8 kDa
Mutation mutation	S174C, C192A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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 BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2eysa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2eysa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2eysb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2eysb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	2eysA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2eysA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2eysB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2eysB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	59.835 Å
Unit-cell length b length_b	131.034 Å
Unit-cell length c length_c	116.852 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	65.510 Å
R factor r_factor	0.2142
R_work r_work	0.2107
R_free r_free	0.2784

fit	/app/data/saxs_computation/ey/2eys/2eys.fit
pddf	/app/data/pr_computation/ey/2eys/2eys.pr.out
profile	/app/data/saxs_computation/ey/2eys/2eys.dat

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition

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

NKT15

State in the Current Structure

Other States of the Same Protein in the Database

NKT15

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)