1bvg
From Proteopedia
| Line 5: | Line 5: | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=DMP:[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)]-2H-1,3-DIAZEPINONE'>DMP</scene> | |LIGAND= <scene name='pdbligand=DMP:[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)]-2H-1,3-DIAZEPINONE'>DMP</scene> | ||
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1bve|1BVE]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvg OCA], [http://www.ebi.ac.uk/pdbsum/1bvg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bvg RCSB]</span> | ||
}} | }} | ||
| Line 34: | Line 37: | ||
[[Category: Wingfield, P.]] | [[Category: Wingfield, P.]] | ||
[[Category: Yamazaki, T.]] | [[Category: Yamazaki, T.]] | ||
| - | [[Category: DMP]] | ||
[[Category: aid]] | [[Category: aid]] | ||
[[Category: aspartyl protease]] | [[Category: aspartyl protease]] | ||
| Line 42: | Line 44: | ||
[[Category: rna-directed dna polymerase]] | [[Category: rna-directed dna polymerase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:09:01 2008'' |
Revision as of 16:09, 30 March 2008
| |||||||
| Ligands: | |||||||
| Activity: | HIV-1 retropepsin, with EC number 3.4.23.16 | ||||||
| Related: | 1BVE
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR MINIMIZED AVERAGE STRUCTURE
Overview
The three-dimensional solution structure of the HIV-1 protease homodimer, MW 22.2 kDa, complexed to a potent, cyclic urea-based inhibitor, DMP323, is reported. This is the first solution structure of an HIV protease/inhibitor complex that has been elucidated. Multidimensional heteronuclear NMR spectra were used to assemble more than 4,200 distance and angle constraints. Using the constraints, together with a hybrid distance geometry/simulated annealing protocol, an ensemble of 28 NMR structures was calculated having no distance or angle violations greater than 0.3 A or 5 degrees, respectively. Neglecting residues in disordered loops, the RMS deviation (RMSD) for backbone atoms in the family of structures was 0.60 A relative to the average structure. The individual NMR structures had excellent covalent geometry and stereochemistry, as did the restrained minimized average structure. The latter structure is similar to the 1.8-A X-ray structure of the protease/DMP323 complex (Chang CH et al., 1995, Protein Science, submitted); the pairwise backbone RMSD calculated for the two structures is 1.22 A. As expected, the mismatch between the structures is greatest in the loops that are disordered and/or flexible. The flexibility of residues 37-42 and 50-51 may be important in facilitating substrate binding and product release, because these residues make up the respective hinges and tips of the protease flaps. Flexibility of residues 4-8 may play a role in protease regulation by facilitating autolysis.
About this Structure
1BVG is a Single protein structure of sequence from Human immunodeficiency virus. Full crystallographic information is available from OCA.
Reference
Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy., Yamazaki T, Hinck AP, Wang YX, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, Kaufman JD, Chang CH, Domaille PJ, Lam PY, Protein Sci. 1996 Mar;5(3):495-506. PMID:8868486
Page seeded by OCA on Sun Mar 30 19:09:01 2008
Categories: HIV-1 retropepsin | Human immunodeficiency virus | Single protein | Chang, C. | Domaille, P J. | Hinck, A P. | Kaufman, J D. | Lam, P Y.S. | Nicholson, L K. | Stahl, S J. | Torchia, D A. | Wang, Y X. | Wingfield, P. | Yamazaki, T. | Aid | Aspartyl protease | Endonuclease | Hydrolase | Polyprotein | Rna-directed dna polymerase
