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Open data
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Basic information
Entry | Database: PDB / ID: 1yek | ||||||
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Title | CATALYTIC ANTIBODY D2.3 COMPLEX | ||||||
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![]() | IMMUNE SYSTEM / ABZYME / REACTION PRODUCT | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gigant, B. / Knossow, M. | ||||||
![]() | ![]() Title: Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody. Authors: Gigant, B. / Charbonnier, J.B. / Eshhar, Z. / Green, B.S. / Knossow, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385 KB | Display | ![]() |
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Full document | ![]() | 393.1 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yeiC ![]() 1yejC ![]() 1yecS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24019.842 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Antibody | Mass: 24189.217 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-NPO / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT ...THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT CHAINS (RESIDUES L107 - L214) HAVE NOT BEEN DETERMINED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH 6.0, 40MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→17 Å / Num. obs: 33481 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.071 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.401 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 84756 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.401 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YEC Resolution: 2.1→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.297 / % reflection Rfree: 5 % / Rfactor Rwork: 0.291 / Rfactor obs: 0.291 |