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- PDB-1vwg: STREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE-BONDED PEP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vwg | |||||||||
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Title | STREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE-BONDED PEPTIDE DIMER OF CYCLO-AC-[CHPQGPPC]-NH2, PH 2.5 | |||||||||
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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 | ![]() | 63.7 KB | Display | ![]() |
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PDB format | ![]() | 48.6 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 | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vwaC ![]() 1vwbC ![]() 1vwcC ![]() 1vwdC ![]() 1vweC ![]() 1vwfC ![]() 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: 863.018 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: 2.64 Å3/Da / Density % sol: 30.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 2.5 Details: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 2.5. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 25029 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Highest resolution: 1.33 Å / Num. measured all: 65678 / Rmerge(I) obs: 0.06 |
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Processing
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Refinement | Resolution: 1.46→7.5 Å / σ(F): 1.9 Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, SIDE CHAIN OF LEU 25, GLY 26, ALA 35, (CB, HB1, HB2 OF ASP 36), ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, SIDE CHAIN OF LEU 25, GLY 26, ALA 35, (CB, HB1, HB2 OF ASP 36), (CG, OD1, AND OD2 OF ASP 36), ALA 46, VAL 47, GLY 48, ASN 49, ALA 50, SIDE CHAIN OF GLU 51, TERMINUS OF ARG 53, SER 63, PRO 64, ALA 65, THR 66, ASP 67, GLY 68, GLY 99, ALA 100, (N AND HN OF GLU 101), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 101), TERMINUS OF ARG 103, (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2 OF GLN 116), (CD, OE1, OE2 OF GLN 116), ALA 117, (CG, HG1, HG2, CD, HD1, HD2 OF LYS 121), (CE, HE1, HE2, NZ, HZ1, HZ2, HZ3 OF LYS 121), (ACE P 0 AND CYS P 1), PRO P 7, (CYS P 8 AND NH2 P 9).
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Refinement step | Cycle: LAST / Resolution: 1.46→7.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.53 Å / % reflection obs: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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