2ADJ |
Crystal structure of monoclonal anti-CD4 antibody Q425 in complex with Calcium |
Summary for 2ADJ
| Related | 2ADG 2ADI |
|---|---|
| Descriptor | Q425 Fab Light chain, Q425 Fab Heavy chain |
| Functional Keywords | anti-cd4, interfacial metal, antibody recognition, immune system |
| Biological source | Mus musculus (house mouse) |
| Total number of polymer chains | 2 |
| Total molecular weight | 47691.15 |
| Authors | Zhou, T.,Hamer, D.H.,Hendrickson, W.A.,Sattentau, Q.J.,Kwong, P.D. (deposition date: 2005-07-20, release date: 2005-09-20, modification date: 2009-02-24) |
| Primary citation | Zhou, T.,Hamer, D.H.,Hendrickson, W.A.,Sattentau, Q.J.,Kwong, P.D. Interfacial metal and antibody recognition. Proc.Natl.Acad.Sci.Usa, 102:14575-14580, 2005 PubMed: 16195378 DOI: 10.1073/pnas.0507267102  Import into Mendeley |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
Download full validation report
More Asymmetric unit images
> Structural details
Entity
| Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| A | Q425 Fab Light chain | polymer | 214 | 23721.3 | 1 | UniProt (Q58EU4) | Mus musculus (house mouse)@PDBj | |
| B | Q425 Fab Heavy chain | polymer | 222 | 23929.8 | 1 | Mus musculus (house mouse)@PDBj | ||
| CALCIUM ION | non-polymer | 40.1 | 1 | |||||
| water | water | 18.0 | 30 |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total molecular weight | 47651.1 | |
| Non-Polymers* | Number of molecules | 1 |
| Total molecular weight | 40.1 | |
| All* | Total molecular weight | 47691.1 |
> Experimental details
Refinement Statistics
| Experimental method: | X-RAY DIFFRACTION (2.9 Å) |
| Cell axes | 97.224 | 97.224 | 110.976 |
| Cell angles | 90.00 | 90.00 | 90.00 |
| Spacegroup | P 43 21 2 | ||
| Resolution limits | 9.98 - 2.90 | ||
| the highest resolution shell value | 3.080 - 2.900 | ||
| R-factor | 0.213 | ||
| R-work | 0.21300 | ||
| the highest resolution shell value | 0.318 | ||
| R-free | 0.30000 | ||
| the highest resolution shell value | 0.458 | ||
| RMSD bond length | 0.008 | ||
| RMSD bond angle | 1.500 | ||
Data Collection Statistics
| Resolution limits | 10.00 - 2.90 |
| the highest resolution shell value | - |
| Number of reflections | 10984 |
| Completeness | 92.0 |
| Redundancy | 5.6 |
| I/sigma(I) | 2 |
Crystallization Conditions
| crystal ID | method | pH | pH range | temperature | unit |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
Crystallization Reagents in Literatures*
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
Annotated Information is extracted from Literature Info*
> Functional details
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0072562 | cellular_component | blood microparticle |
| A | 0009897 | cellular_component | external side of plasma membrane |
| A | 0042571 | cellular_component | immunoglobulin complex, circulating |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0003823 | molecular_function | antigen binding |
| A | 0034987 | molecular_function | immunoglobulin receptor binding |
| A | 0030183 | biological_process | B cell differentiation |
| A | 0050853 | biological_process | B cell receptor signaling pathway |
| A | 0006958 | biological_process | complement activation, classical pathway |
| A | 0042742 | biological_process | defense response to bacterium |
| A | 0045087 | biological_process | innate immune response |
| A | 0006911 | biological_process | phagocytosis, engulfment |
| A | 0006910 | biological_process | phagocytosis, recognition |
| A | 0050871 | biological_process | positive regulation of B cell activation |
Functional Information from PDB Data
| site_id | Number of Residues | Details | ||||||||||
| AC1 | 4 | BINDING SITE FOR RESIDUE CA A 3000 | ||||||||||
| ||||||||||||
Functional Information from PDB atom coordinates for the "HETATM" binding sites
| site_id | Number of Residues | Details |
Functional Information from PROSITE/UniProt
| site_id | Number of Residues | Details |
Functional Information from SwissProt/UniProt
| site_id | Number of Residues | Details |
Catalytic Information from CSA
| site_id | Number of Residues | Details |
Catalytic Information from CATRES
| site_id | Number of Residues | Details |
> Sequence Neighbor
> Downloads
Resources
| File format | File name (file size) | |
| PDB | all | pdb2adj.ent.gz (73.01 KB) |
| all (no-compress) | pdb2adj.ent (302.64 KB) | |
| header only | pdb2adj.ent.gz (7.38 KB) | |
| PDBx/mmCIF | 2adj.cif.gz (93.41 KB) | |
| PDBML | all | 2adj.xml.gz (140.35 KB) |
| no-atom | 2adj-noatom.xml.gz (25.13 KB) | |
| ext-atom | 2adj-extatom.xml.gz (77.82 KB) | |
| PDBMLplus | all | 2adj-plus.xml.gz (141.21 KB) |
| no-atom | 2adj-plus-noatom.xml.gz (25.99 KB) | |
| add only | 2adj-add.xml.gz (882 B) | |
| RDF | 2adj.rdf.gz (50 KB) | |
| Structure factors | r2adjsf.ent.gz (101.25 KB) | |
| Biological unit (PDB format) | 2adj.pdb1.gz (68.21 KB) (A,B) *author and software defined assembly, 2 molecule(s) (dimeric) | |
| Validation reports | 2adj_validation.pdf.gz (259.11 KB) | |
| PDF-full | 2adj_full_validation.pdf.gz (277.56 KB) | |
| XML | 2adj_validation.xml.gz (20.54 KB) | |
| PNG | 2adj_multipercentile_validation.png.gz (153.08 KB) | |
| SVG | 2adj_multipercentile_validation.svg.gz (940 B) | |
| Sequence (fasta) | 2adj_seq.txt | |
