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1cdc

CD2, N-TERMINAL DOMAIN (1-99), TRUNCATED FORM

Method: X-RAY DIFFRACTION Dmax: 72.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CD2

Rattus norvegicus

UniProt P08921

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 23–121 Chain B； UniProt 23–121 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 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 1CDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A64 ENGINEERING A MISFOLDED FORM OF RAT CD2 Deposited 1998-03-05 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；20% MPD, 200MM NACL, 0.1M NACO, PH 4.6
Resolution 2.00 Å R-free 0.273
1A6P ENGINEERING OF A MISFOLDED FORM OF CD2 Deposited 1998-02-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–121（96 aa） Fragment：DOMAIN 1
Chain B 26–121（96 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；20% PEG 4000, 5% GLYCEROL, 0.1M NACO, PH 4.6
Resolution 2.08 Å R-free 0.296
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Chain C 23–121（99 aa） Fragment：DOMAIN 1
Chain D 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 23–121（99 aa） Fragment：DOMAIN 1
Chain D 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1HNG CRYSTAL STRUCTURE AT 2.8 ANGSTROMS RESOLUTION OF A SOLUBLE FORM OF THE CELL ADHESION MOLECULE CD2 Deposited 1994-08-10 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–198（176 aa）
Chain B 23–198（176 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1T6W RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES Deposited 2004-05-07 Different construct Different mutation/modification 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 23–121（99 aa）
Mutation：N15D, N17D CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Pressure 1
NMR sample composition 95% H2O, 5% D2O, protein 1 mM, KCl 130 mM, CaCl2 10 mM, PIPES 20 mM | 95% H2O/5% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name CD2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 23–121 Author chain B； PDBConstruct 1–99； UniProt 23–121

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 1cdc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cdc
Deposition date deposition_date1995-05-23
Structure title titleCD2, N-TERMINAL DOMAIN (1-99), TRUNCATED FORM
Keywords keywordsMISFOLDED, METASTABLE, IMMUNE SYSTEM PROTEIN, RECEPTOR; IMMUNE SYSTEM PROTEIN, RECEPTOR
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_guinier19.13 Å
Radius of gyration Rg (electron density) rg_electron18.32 Å
Forward intensity I(0) i08485880.00
Molecular weight molecular_weight21537.0 kDa
Excluded volume excluded_volume27065 ų
Envelope volume envelope_volume31865 ų
Hydration-shell volume shell_volume15388 ų
Envelope diameter envelope_diameter69.7 Å
Shell Rg shell_rg23.81 Å
Envelope Rg envelope_rg18.72 Å
Shape Rg shape_rg18.30 Å
Total Rg total_rg19.28 Å
Total atoms total_atoms1518
Residues n_residues192
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 dmax72.4 Å
Rg (real space) rg_real19.20 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real8.4860e+06
I(0) uncertainty (real space) i0_real_error1.1030e+05
Rg (reciprocal space) rg_reciprocal19.19 Å
I(0) (reciprocal space) i0_reciprocal8486000.0000
Solution quality estimate total_estimate0.7974
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.1 Å
Skewness Skewness skewness0.507
Kurtosis Kurtosis kurtosis0.012
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4014000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.548; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.723; Smooth: 0.996
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cdca_
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_idd1cdcb_
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 (2 domains)

Domain ID domain_id1cdcA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1cdcB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)