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1hnf

CRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL ADHESION MOLECULE CD2 AT 2.5 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 90.3 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 25–206 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å

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 1HNF 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 ligand/ion Different experimental method Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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
1L2Z CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide Deposited 2002-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 1–182； UniProt 25–206

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 1hnf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1hnf
Deposition date deposition_date1994-08-10
Structure title titleCRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL ADHESION MOLECULE CD2 AT 2.5 ANGSTROMS RESOLUTION
Keywords keywordsT LYMPHOCYTE ADHESION GLYCOPROTEIN; T LYMPHOCYTE ADHESION GLYCOPROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.43 Å
Radius of gyration Rg (electron density) rg_electron24.52 Å
Forward intensity I(0) i07853800.00
Molecular weight molecular_weight21236.0 kDa
Excluded volume excluded_volume26781 ų
Envelope volume envelope_volume33670 ų
Hydration-shell volume shell_volume13380 ų
Envelope diameter envelope_diameter93.7 Å
Shell Rg shell_rg27.60 Å
Envelope Rg envelope_rg24.74 Å
Shape Rg shape_rg24.48 Å
Total Rg total_rg25.10 Å
Total atoms total_atoms1490
Residues n_residues179
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 dmax90.3 Å
Rg (real space) rg_real24.98 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real7.8540e+06
I(0) uncertainty (real space) i0_real_error1.3300e+05
Rg (reciprocal space) rg_reciprocal24.86 Å
I(0) (reciprocal space) i0_reciprocal7853000.0000
Solution quality estimate total_estimate0.6923
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.6 Å
Skewness Skewness skewness0.633
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1625000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.316; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.056; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1hnfa1
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)
Domain ID domain_idd1hnfa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.3 — C2 set domains

CATH v4.4 (2 domains)

Domain ID domain_id1hnfA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hnfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (3)

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9. Files and Curves (10)