1DEE	Immune System	date	Nov 15, 1999
title	Structure Of S. Aureus Protein A Bound To A Human Igm Fab
authors	M.Graille, E.A.Stura, A.L.Corper, B.J.Sutton, M.J.Taussig, J.B.Charbonnier, G.J.Silverman
compound		source
Molecule: Igm Rf 2a2 Chain: A, C, E Fragment: Fab Light Chain		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: Fab Of The V3-30 Vh1.9iii-Encoded 2a2 Igm R Factor Produced By Trypsin Cleavage Of The Igm Secreted By Hybridoma Created From Synovial B Cells Of A Rheumatoid Art Patient;
Molecule: Igm Rf 2a2 Chain: B, D, F Fragment: Fab Heavy Chain		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: Fab Of The V3-30 Vh1.9iii-Encoded 2a2 Igm R Factor Produced By Trypsin Cleavage Of The Igm Secreted By Hybridoma Created From Synovial B Cells Of A Rheumatoid Art Patient;
Molecule: Immunoglobulin G Binding Protein A Chain: G, H Fragment: Recombinant Domain D Engineered: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Expression_system: Staphylococcus Aureus Expression_system_taxid: 1280
symmetry	Space Group: P 1 21 1	R_factor 0.217 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 68.520 78.910 163.240 90.00 100.71 90.00
method	X-Ray Diffraction	resolution	2.70 Å
related structures	by homologous chain: 1FC2, 1HEZ, 1HZH, 1LP1, 1QLR, 1YZZ
Gene Ontology	Chain Function Process Component H, G
Primary reference	Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity., Graille M, Stura EA, Corper AL, Sutton BJ, Taussig MJ, Charbonnier JB, Silverman GJ, Proc Natl Acad Sci U S A 2000 May 9;97(10):5399-404. PMID:10805799

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (226 Kb) [Save to disk] Biological Unit Coordinates (1dee.pdb1.gz) 71 Kb Biological Unit Coordinates (1dee.pdb2.gz) 79 Kb Biological Unit Coordinates (1dee.pdb3.gz) 81 Kb Biological Unit Coordinates (1dee.pdb4.gz) 72 Kb Biological Unit Coordinates (1dee.pdb5.gz) 71 Kb CSU: Contacts of Structural Units for 1DEE Likely Quarternary Molecular Structure file(s) for 1DEE Structure Factors (349 Kb) Retrieve 1DEE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DEE from S2C, [Save to disk] Re-refined 1dee structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DEE in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1DEE

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1DEE, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1deea1, region A:1-107 [Jmol] [rasmolscript] [script source]     - Domain d1deea2, region A:108-214 [Jmol] [rasmolscript] [script source]     - Domain d1deeb1, region B:501-621 [Jmol] [rasmolscript] [script source]     - Domain d1deeb2, region B:622-723 [Jmol] [rasmolscript] [script source]     - Domain d1deec1, region C:1001-1107 [Jmol] [rasmolscript] [script source]     - Domain d1deec2, region C:1108-1214 [Jmol] [rasmolscript] [script source]     - Domain d1deed1, region D:1501-1621 [Jmol] [rasmolscript] [script source]     - Domain d1deed2, region D:1622-1723 [Jmol] [rasmolscript] [script source]     - Domain d1deee1, region E:2001-2107 [Jmol] [rasmolscript] [script source]     - Domain d1deee2, region E:2108-2214 [Jmol] [rasmolscript] [script source]     - Domain d1deef1, region F:2501-2621 [Jmol] [rasmolscript] [script source]     - Domain d1deef2, region F:2622-2723 [Jmol] [rasmolscript] [script source]     - Domain d1deeg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1deeh_, region H [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1dee_E] [1dee_A] [1dee_B] [1dee_G] [1dee] [1dee_D] [1dee_F] [1dee_C] [1dee_H] SWISS-PROT database: [P02976] Domain organization of [SPA_STAA8] by SWISSPFAM Domains found in 1DEE: [IG_like] [IGv ] by SMART

Other resources with information on 1DEE

Community annotation for 1DEE at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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