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Yorodumi- PDB-1c70: ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c70 | ||||||
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Title | ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP. | ||||||
Components | PROTEIN (PROTEASE) | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Munshi, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Authors: Munshi, S. / Chen, Z. / Yan, Y. / Li, Y. / Olsen, D.B. / Schock, H.B. / Galvin, B.B. / Dorsey, B. / Kuo, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c70.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c70.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c70 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c70 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE IS ONE L-756,423 INHIBITOR MOLECULE LABELED AS L75. |
-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NY5 ISOLATE / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: NY5 ISOLATE / Production host: Escherichia coli (E. coli) References: UniProt: O92103, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases #2: Chemical | ChemComp-L75 / | #3: Water | ChemComp-HOH / | Nonpolymer details | L-756,423 IS n-[2(r)-hydroxy-1(s)-indanyl]-2(r)-phenylmethyl -4(s)-hydroxy-5-[4-[2- ...L-756,423 IS n-[2(r)-hydroxy-1(s)-indanyl]-2(r)-phenylmethyl -4(s)-hydroxy-5-[4-[2-benzofuranylmethyl]-2(s)-[tert- butylaminocarbonyl]-piperazinyl]-pentaneamide | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % Description: CRYSTALS OBTAINED BY CO-CRYSTALLIZATION AT PH 5.2, USING 0.6M NaCl AS PRECIPITATING AGENT IN 0.1M SODIUM ACETATE BUFFER. PROTEIN WAS AT 5.5 MG/ML CONCENTRATION. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging dropDetails: inhibitor-protein mixture and the reservoir solution were mixed in a 1:1(v/v) ratio | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. all: 33787 / Num. obs: 7292 / % possible obs: 86 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 78 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 33787 |
Reflection shell | *PLUS % possible obs: 78 % / Num. unique obs: 648 / Num. measured obs: 1291 / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.8 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→8 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.16 / Rfactor obs: 0.16 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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