SAXSdb — 1l2z

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

CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2

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 280–341	Fragment：Residue 1-62	T-CELL SURFACE ANTIGEN CD2 × 1 （P06729）	SOLUTION NMR NMR measurement conditions：pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR measurement conditions：pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR sample composition：1 mM GYF domain U-deuterated, U-15N, 1mM Peptide, 50 mM phosphate buffer, pH 6.3, 100% D2O \| 100% D2O NMR sample composition：1 mM GYF domain, aromatic amino acids protonated only, 1 mM Peptide protonated \| 100% D2O	Resolution not provided

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 1L2Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GYF GYF DOMAIN FROM HUMAN CD2BP2 PROTEIN Deposited 1999-04-30	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 280–341（62 aa） Fragment：CD2-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NAPO4 NMR sample composition 90% WATER/10%D2O	Resolution not provided
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 262–341（80 aa） Fragment：86 amino acid C-terminal fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 262–341（80 aa） Fragment：86 amino acid C-terminal fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 262–341（80 aa） Fragment：86 amino acid C-terminal fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 280–341（62 aa） Fragment：RESIDUES 280-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 280–341（62 aa） Fragment：RESIDUES 280-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
8Q7Q Structure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 2) Deposited 2023-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8Q7V Structure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 1) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8Q7W Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 3) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8Q7X Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8Q91 Structure of the human 20S U5 snRNP core Deposited 2023-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain F 1–341（341 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8RC0 Structure of the human 20S U5 snRNP Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain F 1–341（341 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD2B2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–62； UniProt 280–341

T-CELL SURFACE ANTIGEN CD2

OrganismNot specified

UniProt P06729

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 294–304	Fragment：Residue 63-73	CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2 × 1 （O95400）	SOLUTION NMR NMR measurement conditions：pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR measurement conditions：pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR sample composition：1 mM GYF domain U-deuterated, U-15N, 1mM Peptide, 50 mM phosphate buffer, pH 6.3, 100% D2O \| 100% D2O NMR sample composition：1 mM GYF domain, aromatic amino acids protonated only, 1 mM Peptide protonated \| 100% D2O	Resolution not provided

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 1L2Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CDB STRUCTURE OF THE GLYCOSYLATED ADHESION DOMAIN OF HUMAN T LYMPHOCYTE GLYCOPROTEIN CD2 Deposited 1993-09-15	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–129（105 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1GYA N-GLYCAN AND POLYPEPTIDE NMR SOLUTION STRUCTURES OF THE ADHESION DOMAIN OF HUMAN CD2 Deposited 1995-05-26	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–129（105 aa） Fragment：ADHESION DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；286 K	Resolution not provided
1HNF CRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL ADHESION MOLECULE CD2 AT 2.5 ANGSTROMS RESOLUTION Deposited 1994-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–206（182 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
2J6O ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETEROTRIMER Deposited 2006-10-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 324–333（10 aa） Fragment：CMS BINDING SEQUENCE, RESIDUES 324-333	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG3000, 0.1M ACETATE PH 5.5	Resolution 2.23 Å R-free 0.286
2J7I ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETERODIMER Deposited 2006-10-09	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 324–333（10 aa） Fragment：CMS BINDING SEQUENCE, RESIDUES 324-333	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；30% PEG8000, 0.2M NACL, 0.1M TRIS-HCL PH 8.0	Resolution 2.90 Å R-free 0.295
2J7I ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETERODIMER Deposited 2006-10-09	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 324–333（10 aa） Fragment：CMS BINDING SEQUENCE, RESIDUES 324-333	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；30% PEG8000, 0.2M NACL, 0.1M TRIS-HCL PH 8.0	Resolution 2.90 Å R-free 0.295

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

View Construct and Data Evidence

UniProt name	CD2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 294–304

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	1l2z
Deposition date deposition_date	2002-02-26
Structure title title	CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide
Keywords keywords	GYF domain, protein-protein interaction, proline-rich peptide, CD2, CD2BP2, PEPTIDE BINDING-SIGNALING PROTEIN COMPLEX; PEPTIDE BINDING/SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.07 Å
Radius of gyration Rg (electron density) rg_electron	11.68 Å
Forward intensity I(0) i0	238323000.00
Molecular weight molecular_weight	128230.0 kDa
Excluded volume excluded_volume	158810 Å³
Envelope volume envelope_volume	17112 Å³
Hydration-shell volume shell_volume	11083 Å³
Envelope diameter envelope_diameter	43.1 Å
Shell Rg shell_rg	18.88 Å
Envelope Rg envelope_rg	13.64 Å
Shape Rg shape_rg	11.65 Å
Total Rg total_rg	11.97 Å
Total atoms total_atoms	17385
Residues n_residues	1095
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	40.4 Å
Rg (real space) rg_real	12.02 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.3830e+08
I(0) uncertainty (real space) i0_real_error	2.5990e+06
Rg (reciprocal space) rg_reciprocal	12.02 Å
I(0) (reciprocal space) i0_reciprocal	238300000.0000
Solution quality estimate total_estimate	0.8611
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.192
Kurtosis Kurtosis kurtosis	-0.187
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	182500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1l2za_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

CATH v4.4 (1 domains)

Domain ID domain_id	1l2zA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

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8. Citations (1)

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Description description	CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2
Molecular weight formula_weight	7320.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17385

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)

Description description	T-CELL SURFACE ANTIGEN CD2
Molecular weight formula_weight	1240.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/l2/1l2z/1l2z.fit
pddf	/app/data/pr_computation/l2/1l2z/1l2z.pr.out
profile	/app/data/saxs_computation/l2/1l2z/1l2z.dat

CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide

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

CD2 ANTIGEN (CYTOPLASMIC TAIL)-BINDING PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

T-CELL SURFACE ANTIGEN CD2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)