- PDB-2whh: HIV-1 protease tethered dimer Q-product complex along with nucleo... -
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基本情報
登録情報
データベース: PDB / ID: 2whh
タイトル
HIV-1 protease tethered dimer Q-product complex along with nucleophilic water molecule
要素
POL PROTEIN
キーワード
HYDROLASE / PROTEASE / DRUG DESIGN / TRANSFERASE / NUCLEOTIDYLTRANSFERASE / RNA-DIRECTED DNA POLYMERASE / CATALYTIC MECHANISM / MULTIFUNCTIONAL ENZYME / TRANSITION STATE / ASPARTYL PROTEASE
機能・相同性
機能・相同性情報
integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / peptidase activity / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / 加水分解酵素; エステル加水分解酵素 / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane / metal ion binding 類似検索 - 分子機能
分子量: 21902.760 Da / 分子数: 1 / 断片: RESIDUES 7-105 / 変異: YES / 由来タイプ: 組換発現 詳細: 5 RESIDUE PEPTIDE LINK BETWEEN C TERMINUS OF FIRST SUB-UNIT AND THE N TERMINUS OF THE SECOND SUB-UNIT OF THE DIMER TO PRODUCE A TETHERED DIMER OF HIV-1 PROTEASE (ALSO SEE REMARK 999) 由来: (組換発現) HUMAN IMMUNODEFICIENCY VIRUS 1 (ヒト免疫不全ウイルス) プラスミド: PET11 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) 参照: UniProt: Q9QJ78, UniProt: P04585*PLUS, HIV-1 retropepsin
解像度: 1.69→50 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
Rfactor
反射数
%反射
Selection details
Rfree
0.2556
1013
5 %
RANDOM
Rwork
0.2193
-
-
-
obs
0.2193
20251
99.4 %
-
溶媒の処理
Bsol: 68.3213 Å2 / ksol: 0.379056 e/Å3
原子変位パラメータ
Biso mean: 31 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.85 Å2
-1.466 Å2
0 Å2
2-
-
-0.85 Å2
0 Å2
3-
-
-
1.701 Å2
Refine analyze
Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.19 Å
精密化ステップ
サイクル: LAST / 解像度: 1.69→50 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1514
0
48
187
1749
拘束条件
Refine-ID
タイプ
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.010199
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.57436
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
LS精密化 シェル
解像度: 1.69→1.72 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10