[日本語] English
- PDB-5q03: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5q03
タイトルHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-[5-(2-methylpropyl)thiophen-2-yl]sulfonylurea
要素Fructose-1,6-bisphosphatase 1
キーワードHYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex
機能・相同性
機能・相同性情報


cellular response to raffinose / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / monosaccharide binding ...cellular response to raffinose / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / monosaccharide binding / fructose metabolic process / fructose 6-phosphate metabolic process / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / dephosphorylation / AMP binding / cellular response to cAMP / gluconeogenesis / response to nutrient levels / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-95M / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.31 Å
Model detailsFor D3R project
データ登録者Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
引用ジャーナル: To be published
タイトル: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-[5-(2- ...タイトル: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-[5-(2-methylpropyl)thiophen-2-yl]sulfonylurea
著者: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
履歴
登録2017年4月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年1月9日Provider: repository / タイプ: Initial release
改定 1.12019年1月16日Group: Data collection / カテゴリ: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
改定 1.22019年2月6日Group: Data collection / Database references / Structure summary
カテゴリ: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
改定 1.32021年2月10日Group: Structure summary / カテゴリ: audit_author / Item: _audit_author.identifier_ORCID
改定 1.42024年3月6日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)298,27016
ポリマ-294,8758
非ポリマー3,3958
19,2761070
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,1358
ポリマ-147,4384
非ポリマー1,6974
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15790 Å2
ΔGint-83 kcal/mol
Surface area45950 Å2
手法PISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,1358
ポリマ-147,4384
非ポリマー1,6974
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint-81 kcal/mol
Surface area45520 Å2
手法PISA
単位格子
Length a, b, c (Å)66.435, 294.192, 83.569
Angle α, β, γ (deg.)90.000, 97.560, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 9 through 37 or resid 39...
21(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
31(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
41(chain D and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
51(chain E and (resid 9 through 37 or resid 39...
61(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
71(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
81(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain A and (resid 9 through 37 or resid 39...AA9 - 3710 - 38
12THRTHRGLYGLY(chain A and (resid 9 through 37 or resid 39...AA39 - 6140 - 62
13LYSLYSTYRTYR(chain A and (resid 9 through 37 or resid 39...AA72 - 13973 - 140
14LYSLYSSERSER(chain A and (resid 9 through 37 or resid 39...AA141 - 335142 - 336
21ASPASPLEULEU(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB9 - 3710 - 38
22THRTHRTYRTYR(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB39 - 13940 - 140
23LYSLYSSERSER(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB141 - 335142 - 336
31ASPASPLEULEU(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC9 - 3710 - 38
32THRTHRTYRTYR(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC39 - 13940 - 140
33LYSLYSSERSER(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC141 - 335142 - 336
41ASPASPLEULEU(chain D and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))DD9 - 3710 - 38
42THRTHRTYRTYR(chain D and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))DD39 - 13940 - 140
43LYSLYSSERSER(chain D and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))DD141 - 335142 - 336
51ASPASPLEULEU(chain E and (resid 9 through 37 or resid 39...EE9 - 3710 - 38
52THRTHRGLYGLY(chain E and (resid 9 through 37 or resid 39...EE39 - 6140 - 62
53LYSLYSTYRTYR(chain E and (resid 9 through 37 or resid 39...EE72 - 13973 - 140
54LYSLYSSERSER(chain E and (resid 9 through 37 or resid 39...EE141 - 335142 - 336
61ASPASPLEULEU(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF9 - 3710 - 38
62THRTHRTYRTYR(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF39 - 13940 - 140
63LYSLYSSERSER(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF141 - 335142 - 336
71ASPASPLEULEU(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG9 - 3710 - 38
72THRTHRTYRTYR(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG39 - 13940 - 140
73LYSLYSSERSER(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG141 - 335142 - 336
81ASPASPLEULEU(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH9 - 3710 - 38
82THRTHRTYRTYR(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH39 - 13940 - 140
83LYSLYSSERSER(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH141 - 335142 - 336

-
要素

#1: タンパク質
Fructose-1,6-bisphosphatase 1 / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


分子量: 36859.418 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FBP1, hCG_1640493 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: 化合物
ChemComp-95M / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-5-(2-methylpropyl)thiophene-2-sulfonamide


分子量: 424.357 Da / 分子数: 8 / 由来タイプ: 合成 / : C12H14BrN3O3S3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1070 / 由来タイプ: 天然 / : H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.84 Å3/Da / 溶媒含有率: 56.63 %
結晶化温度: 300 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X10SA / 波長: 0.987 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2005年12月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.987 Å / 相対比: 1
反射解像度: 2.31→20.369 Å / Num. obs: 133552 / % possible obs: 96.71 %

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類NB
PHENIX1.11.1_2575精密化
PDB_EXTRACT3.23データ抽出
精密化構造決定の手法: 分子置換 / 解像度: 2.31→20.369 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 25.72 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2379 6681 5 %
Rwork0.1784 126871 -
obs0.1815 133552 96.71 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 142.59 Å2 / Biso mean: 39.1678 Å2 / Biso min: 6.06 Å2
精密化ステップサイクル: final / 解像度: 2.31→20.369 Å
タンパク質核酸リガンド溶媒全体
原子数19440 0 176 1070 20686
Biso mean--47.76 40.1 -
残基数----2540
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0120015
X-RAY DIFFRACTIONf_angle_d1.06327047
X-RAY DIFFRACTIONf_chiral_restr0.0633056
X-RAY DIFFRACTIONf_plane_restr0.0073454
X-RAY DIFFRACTIONf_dihedral_angle_d10.42712163
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A12159X-RAY DIFFRACTION10.55TORSIONAL
12B12159X-RAY DIFFRACTION10.55TORSIONAL
13C12159X-RAY DIFFRACTION10.55TORSIONAL
14D12159X-RAY DIFFRACTION10.55TORSIONAL
15E12159X-RAY DIFFRACTION10.55TORSIONAL
16F12159X-RAY DIFFRACTION10.55TORSIONAL
17G12159X-RAY DIFFRACTION10.55TORSIONAL
18H12159X-RAY DIFFRACTION10.55TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3103-2.33660.3427840.26871509159335
2.3366-2.3640.30871660.2633172333872
2.364-2.39280.30362060.26294128433494
2.3928-2.4230.34282240.263643484572100
2.423-2.45490.3272470.247644194666100
2.4549-2.48840.34592110.248343274538100
2.4884-2.52390.30762320.249143954627100
2.5239-2.56150.36252540.244843424596100
2.5615-2.60150.31152380.232343124550100
2.6015-2.6440.28442220.224343994621100
2.644-2.68950.29792320.215743914623100
2.6895-2.73830.29872160.211843064522100
2.7383-2.79090.26932340.207944424676100
2.7909-2.84770.29132100.203243434553100
2.8477-2.90940.27342600.193743884648100
2.9094-2.97690.24282310.190343324563100
2.9769-3.05110.29192410.193343244565100
3.0511-3.13330.25582130.183544404653100
3.1333-3.22520.25062190.182343734592100
3.2252-3.32890.24022080.173444354643100
3.3289-3.44730.22992220.174343234545100
3.4473-3.58460.23382250.168443724597100
3.5846-3.74680.22662420.156243604602100
3.7468-3.9430.21022460.156143924638100
3.943-4.1880.20952400.142343994639100
4.188-4.50810.17412320.132343334565100
4.5081-4.95590.16912330.120643814614100
4.9559-5.65950.1882140.143243964610100
5.6595-7.08030.20172410.172943934634100
7.0803-20.36940.18162380.16343974635100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.01330.00020.00640.04820.03470.0343-0.0433-0.0240.0148-0.1211-0.0317-0.0273-0.05640.0373-0.01050.1385-0.02660.01070.11910.02920.164737.214416.5968-5.5514
20.0097-0.0218-0.00520.06550.00780.0069-0.06450.03820.0824-0.0988-0.00320.071-0.070.0285-0.06620.19220.0327-0.06880.09280.03410.203919.57923.561-7.9431
30.00470.00460.00480.0186-0.00340.0146-0.0123-0.00150.037-0.0432-0.01420.0043-0.0142-0.0055-0.0070.31170.0311-0.15690.0280.05430.238117.844932.341-10.3615
40.0128-0.00250.00240.01120.0020.0095-0.006-0.0466-0.0824-0.02160.01880.10980.0152-0.0204-0.0027-0.01620.02280.02180.20060.07220.271312.3513-1.977314.6938
50.00570.00360.00640.00340.00290.01610.0152-0.0102-0.01080.0115-0.00810.00730.0265-0.0160.00920.08270.05140.07980.2207-0.00890.29571.4723-1.616923.7526
60.0673-0.03420.00020.04560.03530.0483-0.0494-0.09850.00280.001-0.05560.0915-0.1058-0.0493-0.1038-0.00070.12250.01920.1181-0.05570.26089.858919.651616.2938
70.009-0.0055-0.01260.00370.00060.0199-0.0041-0.0274-0.0380.00320.01430.0654-0.0297-0.02910.00930.01090.09920.01650.2022-0.08270.39550.663119.640117.68
80.0114-0.0041-0.00520.02890.01760.0185-0.02280.026-0.0428-0.1166-0.02520.03180.0133-0.0078-0.01190.12080.05170.03770.1350.03140.114735.9037-9.4277-11.3696
90.0121-0.0261-0.02330.0220.01940.01170.03430.0623-0.054-0.1432-0.0022-0.070.09160.12870.0673-0.02380.11460.17830.137-0.01870.028853.7014-19.3924-7.0035
100.0158-0.01070.00390.0161-0.00640.0069-0.0297-0.04570.02320.07020.0328-0.0305-0.0004-0.007-0.00290.0050.06780.05940.15270.01720.056136.6862-5.488524.0849
110.03250.0020.02230.0222-0.01320.0323-0.0171-0.0575-0.0210.05180.03130.00920.08210.01780.0190.07660.04110.0150.12570.0240.100641.1361-23.573720.615
120.0039-0.0051-0.00390.0060.00440.0157-0.0241-0.04050.00340.04910.0196-0.04240.07560.0254-0.00210.16350.0870.00260.14990.02460.139847.3465-27.879424.8893
130.06460.05450.01740.07570.02510.02070.0558-0.0342-0.16540.06030.0433-0.05020.02620.01310.06930.2798-0.0151-0.0780.0270.07540.1384-3.363549.185644.1518
140.00110.0036-0.00010.03-0.02480.02340.01320.0011-0.070.02270.00290.0447-0.0234-0.03110.00170.1389-0.0871-0.00150.13630.00110.2359-26.850445.687537.537
150.00250.00140.00450.0075-0.00350.00430.0315-0.0051-0.04760.025-0.02730.01460.0298-0.028500.304-0.0871-0.00640.15580.03470.4213-21.24236.677243.0122
160.01130.01210.0060.00980.00160.0042-0.01650.07890.01820.0301-0.00860.0887-0.03390.0215-00.28620.0069-0.04360.2032-0.02130.1716-14.098370.850117.9705
170.0080.00520.00560.00380.0040.00390.01420.016-0.0175-0.0107-0.0130.0025-0.0239-0.0214-00.45820.0509-0.06680.4270.07310.3542-26.760271.040916.5301
180.0230.01270.00590.0068-0.00140.01670.02250.083-0.04140.00030.00770.0174-0.03110.00220.06760.14860.0036-0.07580.2208-0.09160.1292-18.923659.909211.0839
190.00420.0015-0.00110.00270.00250.00210.01660.00780.00190.00260.02340.0016-0.0058-0.00270.00010.2659-0.0895-0.02980.3294-0.16940.4825-30.767136.269419.8899
200.00530.00410.00650.00320.00030.00380.00570.0768-0.02740.01570.03170.02610.002-0.0506-00.20190.01-0.09950.2952-0.090.3386-30.285349.778611.6607
210.01340.0117-0.00030.03530.00180.00250.046-0.02870.02240.0036-0.03010.0422-0.0243-0.0203-0.00990.2719-0.05580.01380.07520.01340.0761-3.38975.817148.8846
220.00890.00180.00170.01440.0070.00350.029-0.01420.0502-0.0356-0.01540.0101-0.001-0.0026-00.3357-0.13570.01750.2125-0.00430.13720.053284.11155.8442
230.0366-0.02240.00120.0135-0.00080.01420.0446-0.0210.03350.0658-0.0233-0.03180.02990.10140.00060.2633-0.0743-0.00850.15650.00180.101816.632385.963345.2613
240.00230.00260.00170.00230.0040.0027-0.0302-0.01740.00560.0311-0.0566-0.0084-0.02950.0148-00.2084-0.1164-0.01950.21080.00220.155620.146793.143455.1125
250.00680.0007-0.00790.0056-0.00080.006-0.02070.0523-0.0087-0.03780.056-0.0230.022-0.015200.3249-0.0263-0.0290.1823-0.01010.10512.344473.205816.5073
260.00790.0009-0.00210.0084-0.0050.0040.01830.0117-0.0357-0.0337-0.0159-0.0220.00620.0161-00.4814-0.04330.04350.39470.01320.218814.261574.64912.3264
270.00510.00410.00170.0066-0.00180.0020.0037-0.0113-0.01070.0052-0.019-0.0230.00250.0089-00.325-0.02660.03980.2563-0.00760.126312.311580.20593.6275
280.0570.02080.03030.0110.00880.01490.05080.05160.011-0.07020.02530.01250.01140.01750.01560.2759-0.06970.01440.14480.00640.07784.308988.186217.8084
290.00530.0019-0.00280.0028-0.00420.0052-0.013-0.0016-0.0122-0.0017-0.04440.0189-0.02820.0067-00.2943-0.08480.06450.20770.01760.209120.8995103.754530.525
300.00640.00020.00780.0042-0.0070.01120.02930.0386-0.0039-0.03060.0322-0.06790.01790.03700.3833-0.07790.03330.21820.01280.173217.718996.020317.1058
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 122 )A9 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 247 )A123 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 335 )A248 - 335
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 131 )B9 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 148 )B132 - 148
6X-RAY DIFFRACTION6chain 'B' and (resid 149 through 247 )B149 - 247
7X-RAY DIFFRACTION7chain 'B' and (resid 248 through 335 )B248 - 335
8X-RAY DIFFRACTION8chain 'C' and (resid 9 through 131 )C9 - 131
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 335 )C132 - 335
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 131 )D9 - 131
11X-RAY DIFFRACTION11chain 'D' and (resid 132 through 247 )D132 - 247
12X-RAY DIFFRACTION12chain 'D' and (resid 248 through 335 )D248 - 335
13X-RAY DIFFRACTION13chain 'E' and (resid 9 through 179 )E9 - 179
14X-RAY DIFFRACTION14chain 'E' and (resid 180 through 247 )E180 - 247
15X-RAY DIFFRACTION15chain 'E' and (resid 248 through 335 )E248 - 335
16X-RAY DIFFRACTION16chain 'F' and (resid 9 through 88 )F9 - 88
17X-RAY DIFFRACTION17chain 'F' and (resid 89 through 131 )F89 - 131
18X-RAY DIFFRACTION18chain 'F' and (resid 132 through 212 )F132 - 212
19X-RAY DIFFRACTION19chain 'F' and (resid 213 through 247 )F213 - 247
20X-RAY DIFFRACTION20chain 'F' and (resid 248 through 335 )F248 - 335
21X-RAY DIFFRACTION21chain 'G' and (resid 9 through 106 )G9 - 106
22X-RAY DIFFRACTION22chain 'G' and (resid 107 through 155 )G107 - 155
23X-RAY DIFFRACTION23chain 'G' and (resid 156 through 290 )G156 - 290
24X-RAY DIFFRACTION24chain 'G' and (resid 291 through 335 )G291 - 335
25X-RAY DIFFRACTION25chain 'H' and (resid 9 through 88 )H9 - 88
26X-RAY DIFFRACTION26chain 'H' and (resid 89 through 131 )H89 - 131
27X-RAY DIFFRACTION27chain 'H' and (resid 132 through 148 )H132 - 148
28X-RAY DIFFRACTION28chain 'H' and (resid 149 through 212 )H149 - 212
29X-RAY DIFFRACTION29chain 'H' and (resid 213 through 247 )H213 - 247
30X-RAY DIFFRACTION30chain 'H' and (resid 248 through 335 )H248 - 335

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る