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1cdb

STRUCTURE OF THE GLYCOSYLATED ADHESION DOMAIN OF HUMAN T LYMPHOCYTE GLYCOPROTEIN CD2

Method: SOLUTION NMR Dmax: 38.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CD2

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 25–129 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions 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 1CDB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 ligand/ion Different experimental method 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
1L2Z CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide Deposited 2002-02-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 294–304（11 aa） Fragment：Residue 63-73
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；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
2J6O ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETEROTRIMER Deposited 2006-10-02 Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–105； UniProt 25–129

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1cdb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cdb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cdb
Deposition date deposition_date1993-09-15
Structure title titleSTRUCTURE OF THE GLYCOSYLATED ADHESION DOMAIN OF HUMAN T LYMPHOCYTE GLYCOPROTEIN CD2
Keywords keywordsT LYMPHOCYTE ADHESION GLYCOPROTEIN; T LYMPHOCYTE ADHESION GLYCOPROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.09 Å
Radius of gyration Rg (electron density) rg_electron14.73 Å
Forward intensity I(0) i0645211000.00
Molecular weight molecular_weight223760.0 kDa
Excluded volume excluded_volume283990 ų
Envelope volume envelope_volume37708 ų
Hydration-shell volume shell_volume17706 ų
Envelope diameter envelope_diameter60.3 Å
Shell Rg shell_rg24.19 Å
Envelope Rg envelope_rg18.48 Å
Shape Rg shape_rg14.66 Å
Total Rg total_rg15.22 Å
Total atoms total_atoms15786
Residues n_residues1890
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax38.1 Å
Rg (real space) rg_real14.37 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real6.1630e+08
I(0) uncertainty (real space) i0_real_error4.6220e+06
Rg (reciprocal space) rg_reciprocal15.10 Å
I(0) (reciprocal space) i0_reciprocal645200000.0000
Solution quality estimate total_estimate0.6881
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.4 Å
Skewness Skewness skewness0.144
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.1080
Highest regularization parameter α highest_alpha270500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.999; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cdba_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (1 domains)

Domain ID domain_id1cdbA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (2)

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9. Files and Curves (10)