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Open data
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Basic information
Entry | Database: PDB / ID: 1kcs | ||||||
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Title | CRYSTAL STRUCTURE OF ANTIBODY PC282 IN COMPLEX WITH PS1 PEPTIDE | ||||||
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![]() | IMMUNE SYSTEM / ANTIBODY / PEPTIDE ANTIGEN COMPLEX (ANTIBODY-PEPTIDE) | ||||||
Function / homology | ![]() caveolin-mediated endocytosis of virus by host cell / immunoglobulin complex / immunoglobulin mediated immune response / B cell differentiation / antigen binding / blood microparticle / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane ...caveolin-mediated endocytosis of virus by host cell / immunoglobulin complex / immunoglobulin mediated immune response / B cell differentiation / antigen binding / blood microparticle / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane / plasma membrane 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 | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.1 KB | Display | ![]() |
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Full document | ![]() | 404.9 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 22983.266 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 22760.301 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein/peptide | Mass: 1584.622 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Hepatitis B virus. References: GenBank: 15419846, UniProt: Q91C35*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 20% 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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 14014 / % possible obs: 84 % / Redundancy: 4.5 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 4.9 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. all: 62432 / % possible obs: 84 % |
Reflection shell | *PLUS % possible obs: 83.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.1 |
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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: 46.4748 Å2 / ksol: 0.301772 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor obs: 0.209 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.325 / Rfactor obs: 0.309 |