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Yorodumi- PDB-1ifh: A DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ifh | ||||||
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Title | A DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTIBODY: X-RAY STRUCTURES OF ANTI-PEPTIDE FAB 17(SLASH)9 AND THREE DIFFERENT FAB-PEPTIDE COMPLEXES | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Schulze-Gahmen, U. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes. Authors: Schulze-Gahmen, U. / Rini, J.M. / Wilson, I.A. #1: Journal: Science / Year: 1992 Title: Structural Evidence for Induced Fit as a Mechanism for Antibody-Antigen Recognition Authors: Rini, J.M. / Schulze-Gahmen, U. / Wilson, I.A. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Preliminary Crystallographic Data, Primary Sequence, and Binding Data for an Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Virus Hemagglutinin Authors: Schulze-Gahmen, U. / Rini, J.M. / Arevalo, J. / Stura, E.A. / Kenten, J.H. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifh.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifh.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ifh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifh ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 4: ARG L 211 - ASN L 212 OMEGA ANGLE = 0.020 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151 / 7: CIS PROLINE - PRO H 200 |
-Components
#1: Antibody | Mass: 24025.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: A31790 |
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#2: Antibody | Mass: 23677.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: GenBank: 533229 |
#3: Protein/peptide | Mass: 791.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THERE IS ONE BOUND WATER MOLECULE IN THE BINDING SITE OF THE FAB FRAGMENT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.3 / Method: vapor diffusion, sitting drop / Details: micro seeding | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 9999 Å / Num. obs: 11779 / Num. measured all: 57732 / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 57732 / σ(F): 2 / Rfactor obs: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.6 |