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- PDB-1cdb: STRUCTURE OF THE GLYCOSYLATED ADHESION DOMAIN OF HUMAN T LYMPHOCY... -

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Basic information

Entry
Database: PDB / ID: 1cdb
TitleSTRUCTURE OF THE GLYCOSYLATED ADHESION DOMAIN OF HUMAN T LYMPHOCYTE GLYCOPROTEIN CD2
ComponentsCD2
KeywordsT LYMPHOCYTE ADHESION GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / cell-cell adhesion ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / cell-cell adhesion / receptor tyrosine kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / signaling receptor activity / cell surface receptor signaling pathway / immune response / signaling receptor binding / external side of plasma membrane / apoptotic process / cell surface / Golgi apparatus / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsWyss, D.F. / Withka, J.M. / Recny, M.A. / Wagner, G.
Citation
Journal: Structure / Year: 1993
Title: Structure of the glycosylated adhesion domain of human T lymphocyte glycoprotein CD2.
Authors: Withka, J.M. / Wyss, D.F. / Wagner, G. / Arulanandam, A.R. / Reinherz, E.L. / Recny, M.A.
#1: Journal: Biochemistry / Year: 1993
Title: 1H Resonance Assignments and Secondary Structure of the 13.6 KDa Glycosylated Adhesion Domain of Human CD2
Authors: Wyss, D.F. / Withka, J.M. / Knoppers, M.H. / Sterne, K.A. / Recny, M.A. / Wagner, G.
History
DepositionSep 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2


Theoretical massNumber of molelcules
Total (without water)12,4531
Polymers12,4531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: HIS 72 - LEU 73 MODEL 2 OMEGA =147.36 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: LEU 73 - LYS 74 MODEL 2 OMEGA =140.50 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: LYS 74 - THR 75 MODEL 2 OMEGA =149.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: LEU 73 - LYS 74 MODEL 3 OMEGA =128.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ALA 6 - LEU 7 MODEL 4 OMEGA =126.22 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: TRP 35 - GLU 36 MODEL 4 OMEGA =215.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ASP 58 - THR 59 MODEL 4 OMEGA =131.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: SER 23 - PHE 24 MODEL 6 OMEGA =149.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: LEU 13 - GLY 14 MODEL 7 OMEGA =213.37 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: ARG 48 - LYS 49 MODEL 7 OMEGA =215.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: ASP 58 - THR 59 MODEL 7 OMEGA =135.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ILE 70 - LYS 71 MODEL 7 OMEGA =218.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: LEU 73 - LYS 74 MODEL 7 OMEGA =217.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: LYS 37 - THR 38 MODEL 9 OMEGA =101.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: PHE 54 - LYS 55 MODEL 9 OMEGA =144.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
16: LYS 57 - ASP 58 MODEL 9 OMEGA =210.13 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: GLU 50 - LYS 51 MODEL 11 OMEGA =212.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
18: ASP 58 - THR 59 MODEL 11 OMEGA =141.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: ASP 58 - THR 59 MODEL 13 OMEGA =114.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: TYR 60 - LYS 61 MODEL 13 OMEGA =147.74 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
21: PHE 63 - LYS 64 MODEL 13 OMEGA =122.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
22: ILE 70 - LYS 71 MODEL 13 OMEGA =211.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
23: LEU 73 - LYS 74 MODEL 16 OMEGA =215.49 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
24: ASP 58 - THR 59 MODEL 17 OMEGA =218.09 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
25: LYS 57 - ASP 58 MODEL 18 OMEGA =134.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
26: ASP 58 - THR 59 MODEL 18 OMEGA =107.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / -
Representative

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Components

#1: Protein CD2


Mass: 12453.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / Organ: OVARY / References: UniProt: P06729

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: DGII / Developer: BIOSYM TECHNOLOGIES / Classification: refinement
NMR ensembleConformers submitted total number: 18

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