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Open data
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Basic information
Entry | Database: PDB / ID: 1vwd | ||||||
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Title | STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.0 | ||||||
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![]() | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / CYCLIC PEPTIDE DISCOVERED BY PHAGE DISPLAY / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Katz, B.A. / Cass, R.T. | ||||||
![]() | ![]() Title: In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0. Authors: Katz, B.A. / Cass, R.T. #1: ![]() Title: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity Authors: Katz, B.A. / Liu, B. / Cass, R.T. #2: ![]() Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design Authors: Katz, B.A. #3: ![]() Title: Topochemical Catalysis Achieved by Structure-Based Ligand Design Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #4: ![]() Title: Topochemistry for Preparing Ligands that Dimerize Receptors Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #5: ![]() Title: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence Authors: Katz, B.A. #6: ![]() Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.1 KB | Display | ![]() |
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PDB format | ![]() | 35.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.8 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vwaC ![]() 1vwbC ![]() 1vwcC ![]() 1vweC ![]() 1vwfC ![]() 1vwgC ![]() 1vwhC ![]() 1vwiC ![]() 1vwjC ![]() 1vwkC ![]() 1vwlC ![]() 1vwmC ![]() 1vwnC ![]() 1vwoC ![]() 1vwpC ![]() 1vwqC ![]() 1vwrC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12965.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein/peptide | Mass: 758.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 37.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.0. | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 12200 / Redundancy: 4 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Highest resolution: 1.81 Å / Num. measured all: 49331 / Rmerge(I) obs: 0.06 |
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Processing
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Refinement | Resolution: 1.87→7.5 Å / σ(F): 2 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, SIDE CHAIN OF GLN 24, TERMINUS OF ASP 36, 46, SIDE CHAIN OF 47, 48, 49, 50, 51 (EXCLUDING C AND O), TERMINUS OF ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, SIDE CHAIN OF GLN 24, TERMINUS OF ASP 36, 46, SIDE CHAIN OF 47, 48, 49, 50, 51 (EXCLUDING C AND O), TERMINUS OF ARG 53, 64, 65, 66, 67, 100 AND N OF 101, SIDE CHAIN OF 101, TERMINUS OF ARG 103, TERMINUS OF GLU 116, TERMINUS OF LYS 121, ACE P 0 AND CYS P 1, CYS P 6 AND NH2 P 7. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE 43, 73, 84, 87, 107, 132. DISORDERED WATERS ARE HOH 207 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 354; HOH 331 WHICH OCCUPIES SPACE AVAILABLE WHEN LYS 132 IS IN DISCRETE CONFORMATION NO. 1; HOH 426 WHICH OCCUPIES SPACE AVAILABLE WHEN ARG 84 IS IN DISCRETE CONFORMATION NO. 2. HOH 279, HOH 305, HOH 313, AND HOH 485 ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY. NO ENERGY INTERACTIONS INVOLVING HOH 279, HOH 305, HOH 313 OR HOH 485 WERE TURNED ON DURING REFINEMENT. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, SIDE CHAIN OF GLN 24, TERMINUS OF ASP 36, 46, SIDE CHAIN OF 47, 48, 49, 50, 51 (EXCLUDING C AND O), TERMINUS OF ARG 53, 64, 65, 66, 67, 100 AND N OF 101, SIDE CHAIN OF 101, TERMINUS OF ARG 103, TERMINUS OF GLU 116, TERMINUS OF LYS 121, ACE P 0 AND CYS P 1, CYS P 6 AND NH2 P 7.
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Refinement step | Cycle: LAST / Resolution: 1.87→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.95 Å / % reflection obs: 36.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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