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Open data
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Basic information
Entry | Database: PDB / ID: 1kcu | ||||||
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Title | CRYSTAL STRUCTURE OF ANTIBODY PC287 | ||||||
![]() | (PC287 IMMUNOGLOBULIN) x 2 | ||||||
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Function / homology | ![]() Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V.S. / Salunke, D.M. | ||||||
![]() | ![]() Title: Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. Authors: Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / Salunke, D.M. #1: ![]() Title: Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-antibody Recognition Authors: Nair, D.T. / Singh, K. / Sahu, N. / Rao, K.V. / Salunke, D.M. | ||||||
History |
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Remark 999 | SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the ...SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the time of processing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 23478.830 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23205.986 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 15% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19589 / % possible obs: 85 % / Redundancy: 8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 14215 / % possible obs: 85 % / Num. measured all: 157194 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 81.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8358 Å2 / ksol: 0.305654 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork![]() | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 403 / Rfactor Rwork: 0.381 / Rfactor obs: 0.381 |