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- PDB-6zfh: Structure of human galactokinase in complex with galactose and 2'... -

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基本情報

登録情報
データベース: PDB / ID: 6zfh
タイトルStructure of human galactokinase in complex with galactose and 2'-(benzo[d]oxazol-2-ylamino)-7',8'-dihydro-1'H-spiro[cyclopentane-1,4'-quinazolin]-5'(6'H)-one
要素Galactokinase
キーワードTRANSFERASE / GHMP Kinase / Galactose metabolism / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
機能・相同性
機能・相同性情報


glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / extracellular exosome ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
類似検索 - ドメイン・相同性
beta-D-galactopyranose / Chem-QV2 / Galactokinase
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: 2.439 Å
データ登録者Bezerra, G.A. / Mackinnon, S. / Zhang, M. / Foster, W. / Bailey, H. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Lai, K. / Yue, W.W. / Structural Genomics Consortium (SGC)
資金援助 英国, 1件
組織認可番号国
Wellcome Trust106169/ZZ14/Z 英国
引用ジャーナル: Acs Chem.Biol. / 年: 2021
タイトル: Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia.
著者: Mackinnon, S.R. / Krojer, T. / Foster, W.R. / Diaz-Saez, L. / Tang, M. / Huber, K.V.M. / von Delft, F. / Lai, K. / Brennan, P.E. / Arruda Bezerra, G. / Yue, W.W.
履歴
登録2020年6月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年6月30日Provider: repository / タイプ: Initial release
改定 1.12021年7月28日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年1月24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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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

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集合体

登録構造単位
A: Galactokinase
B: Galactokinase
C: Galactokinase
D: Galactokinase
E: Galactokinase
F: Galactokinase
G: Galactokinase
H: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)348,62023
ポリマ－344,8248
非ポリマー3,79615
水5,981332
1
A: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,6203
ポリマ－43,1031
非ポリマー5172
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Galactokinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,2832
ポリマ－43,1031
非ポリマー1801
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)119.872, 97.204, 144.812
Angle α, β, γ (deg.)90.000, 98.510, 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 7 or (resid 8 and (name...
21(chain B and (resid 7 or (resid 8 and (name...
31(chain C and (resid 7 or (resid 8 and (name...
41(chain D and (resid 7 or (resid 8 and (name...
51(chain E and (resid 7 or (resid 8 and (name...
61(chain F and (resid 7 through 22 or (resid 23...
71(chain G and (resid 7 through 14 or (resid 15...
81(chain H and (resid 7 or (resid 8 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 or (resid 8 and (name...A7
121(chain A and (resid 7 or (resid 8 and (name...A8
131(chain A and (resid 7 or (resid 8 and (name...A3 - 393
141(chain A and (resid 7 or (resid 8 and (name...A3 - 393
151(chain A and (resid 7 or (resid 8 and (name...A3 - 393
161(chain A and (resid 7 or (resid 8 and (name...A3 - 393
211(chain B and (resid 7 or (resid 8 and (name...B7
221(chain B and (resid 7 or (resid 8 and (name...B8
231(chain B and (resid 7 or (resid 8 and (name...B4 - 393
241(chain B and (resid 7 or (resid 8 and (name...B4 - 393
251(chain B and (resid 7 or (resid 8 and (name...B4 - 393
261(chain B and (resid 7 or (resid 8 and (name...B4 - 393
311(chain C and (resid 7 or (resid 8 and (name...C7
321(chain C and (resid 7 or (resid 8 and (name...C8
331(chain C and (resid 7 or (resid 8 and (name...C1 - 393
341(chain C and (resid 7 or (resid 8 and (name...C1 - 393
351(chain C and (resid 7 or (resid 8 and (name...C1 - 393
361(chain C and (resid 7 or (resid 8 and (name...C1 - 393
411(chain D and (resid 7 or (resid 8 and (name...D7
421(chain D and (resid 7 or (resid 8 and (name...D8
431(chain D and (resid 7 or (resid 8 and (name...D4 - 393
441(chain D and (resid 7 or (resid 8 and (name...D4 - 393
451(chain D and (resid 7 or (resid 8 and (name...D4 - 393
461(chain D and (resid 7 or (resid 8 and (name...D4 - 393
511(chain E and (resid 7 or (resid 8 and (name...E7
521(chain E and (resid 7 or (resid 8 and (name...E8
531(chain E and (resid 7 or (resid 8 and (name...E3 - 393
541(chain E and (resid 7 or (resid 8 and (name...E3 - 393
551(chain E and (resid 7 or (resid 8 and (name...E3 - 393
561(chain E and (resid 7 or (resid 8 and (name...E3 - 393
611(chain F and (resid 7 through 22 or (resid 23...F7 - 22
621(chain F and (resid 7 through 22 or (resid 23...F23 - 24
631(chain F and (resid 7 through 22 or (resid 23...F3 - 393
641(chain F and (resid 7 through 22 or (resid 23...F3 - 393
651(chain F and (resid 7 through 22 or (resid 23...F3 - 393
661(chain F and (resid 7 through 22 or (resid 23...F3 - 393
711(chain G and (resid 7 through 14 or (resid 15...G7 - 14
721(chain G and (resid 7 through 14 or (resid 15...G15 - 19
731(chain G and (resid 7 through 14 or (resid 15...G6 - 393
741(chain G and (resid 7 through 14 or (resid 15...G6 - 393
751(chain G and (resid 7 through 14 or (resid 15...G6 - 393
761(chain G and (resid 7 through 14 or (resid 15...G6 - 393
811(chain H and (resid 7 or (resid 8 and (name...H7
821(chain H and (resid 7 or (resid 8 and (name...H8
831(chain H and (resid 7 or (resid 8 and (name...H7 - 393
841(chain H and (resid 7 or (resid 8 and (name...H7 - 393
851(chain H and (resid 7 or (resid 8 and (name...H7 - 393
861(chain H and (resid 7 or (resid 8 and (name...H7 - 393

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要素

#1: タンパク質
Galactokinase / Galactose kinase


分子量: 43102.977 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: GALK1, GALK / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P51570, galactokinase
#2: 糖
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / β-D-ガラクトピラノ-ス


タイプ: D-saccharide, beta linking / 分子量: 180.156 Da / 分子数: 8 / 由来タイプ: 組換発現 / 式: C6H12O6
識別子タイププログラム
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 化合物
ChemComp-QV2 / 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclopentane]-5-one


分子量: 336.388 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C19H20N4O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 332 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.42 Å3/Da / 溶媒含有率: 49.17 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: Morpheus condition: Buffer system 1: 0.1 M pH 6.5, Imidazole; MES monohydrate (acid) Amino acids: 0.02M L-Na-Glutamate; 0.02M Alanine (racemic); 0.02M Glycine; 0.02M Lysine HCl (racemic); 0. ...詳細: Morpheus condition: Buffer system 1: 0.1 M pH 6.5, Imidazole; MES monohydrate (acid) Amino acids: 0.02M L-Na-Glutamate; 0.02M Alanine (racemic); 0.02M Glycine; 0.02M Lysine HCl (racemic); 0.02M Serine (racemic) Precipitant Mix 1: 20% v/v PEG 500 MME; 10 % w/v PEG 20000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年7月30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: 0.9763 Å / 相対比: 1
反射解像度: 2.439→98.79 Å / Num. obs: 121943 / % possible obs: 99.3 % / 冗長度: 6.6 % / Biso Wilson estimate: 41.59 Å2 / Rpim(I) all: 0.126 / Rrim(I) all: 0.325 / Net I/σ(I): 6
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.44-2.486.713958959331.3753.56196.9
6.62-98.876.416.24028663350.0290.073100

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解析

ソフトウェア
名称バージョン分類
xia2データスケーリング
PHENIX1.13_2998精密化
PDB_EXTRACT3.24データ抽出
Aimlessデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1WUU

1wuu


解像度: 2.439→98.787 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 30.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2619 5980 4.92 %
Rwork0.2097 115647 -
obs0.2122 121627 99.06 %
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: 140.95 Å2 / Biso mean: 58.6014 Å2 / Biso min: 18.36 Å2
精密化ステップサイクル: final / 解像度: 2.439→98.787 Å
タンパク質核酸リガンド溶媒全体
原子数22210 0 271 332 22813
Biso mean--60.1 45.11 -
残基数----3074
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A9016X-RAY DIFFRACTION5.013TORSIONAL
12B9016X-RAY DIFFRACTION5.013TORSIONAL
13C9016X-RAY DIFFRACTION5.013TORSIONAL
14D9016X-RAY DIFFRACTION5.013TORSIONAL
15E9016X-RAY DIFFRACTION5.013TORSIONAL
16F9016X-RAY DIFFRACTION5.013TORSIONAL
17G9016X-RAY DIFFRACTION5.013TORSIONAL
18H9016X-RAY DIFFRACTION5.013TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.46630.39612110.3486365595
2.4663-2.49540.36142070.3271384898
2.4954-2.52580.34462020.3103377698
2.5258-2.55780.33132030.3093383299
2.5578-2.59140.38761920.3029378998
2.5914-2.62690.36661880.3042385999
2.6269-2.66450.32521940.2965380598
2.6645-2.70420.33532050.2921380899
2.7042-2.74650.35661850.2779381599
2.7465-2.79150.30851990.2731387699
2.7915-2.83970.33922020.2687382899
2.8397-2.89130.33511810.2572382799
2.8913-2.94690.29222010.2587387899
2.9469-3.00710.2961920.2494385399
3.0071-3.07250.28582100.2508382099
3.0725-3.14390.29712080.2443385499
3.1439-3.22260.27382080.2384385399
3.2226-3.30970.2921900.2293382099
3.3097-3.40710.31882130.2221384799
3.4071-3.51710.28552050.2077387299
3.5171-3.64280.251910.1946387299
3.6428-3.78860.23471890.1887389799
3.7886-3.96110.24282070.18943860100
3.9611-4.16990.2131920.16363901100
4.1699-4.43120.19661820.15773918100
4.4312-4.77330.21341800.14623914100
4.7733-5.25360.19381880.15923917100
5.2536-6.01380.23172060.18513949100
6.0138-7.57630.22962110.1873927100
7.5763-98.780.21632380.1705397799
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.67625.999-0.5627.5418-0.52362.16380.16910.14750.828-0.2211-0.14580.8526-0.0624-0.39180.06960.19730.0946-0.04830.470.0160.4138-29.525811.4739-31.6642
25.90310.30130.83530.9585-0.23571.41820.00910.4995-0.532-0.25020.03360.24670.06-0.1189-0.04910.27560.0354-0.07150.4879-0.01810.3034-20.8576-0.7813-38.5659
36.60370.70630.52763.75980.06851.70410.1982-0.1448-0.8979-0.0647-0.02480.12480.32050.0395-0.17840.20440.0257-0.04670.5466-0.03370.3076-19.1836-4.4916-34.6582
47.76940.29990.18594.5371.55572.27010.0496-0.2394-0.43330.1276-0.0833-0.23110.32350.11310.0710.2538-0.0346-0.03750.36920.10050.266-4.9267-0.1912-29.1496
52.0205-2.3144-0.57815.9785-0.73950.78630.33190.5513-0.1801-0.6634-0.27920.18480.22030.2952-0.03340.23960.0377-0.02060.7632-0.02060.2148-1.22486.5725-41.296
61.7161-1.7253-0.33293.42192.05322.30030.62280.0309-0.6427-0.81-0.1501-0.59150.38880.9523-0.43010.43080.22020.0611.1939-0.00310.448615.9646-6.0001-41.6997
71.4-0.93950.19383.25430.2521.0750.26190.43790.1628-0.3704-0.3428-0.2967-0.07850.30410.04150.2669-0.00720.03610.6730.1830.29926.153611.9176-38.0746
84.56922.0852-0.66338.1313-0.15883.7321-0.0027-0.26510.8827-0.0939-0.17220.2878-0.36460.2380.16950.16460.0061-0.01030.44240.07240.3279-3.656125.7629-34.4383
93.83293.8583-0.60246.6727-1.80891.13950.1075-0.21360.6182-0.0116-0.20670.65380.0190.10850.02280.24720.1164-0.04150.4519-0.00940.3435-13.872114.6636-32.3727
106.85570.85831.83121.578-0.02122.26720.00560.16480.1777-0.0789-0.03170.310.0782-0.24570.01330.2111-0.0258-0.00780.44550.01820.2978-55.8459-46.7278-20.4157
112.9734-0.3704-0.13711.61380.06581.8245-0.08570.44050.3857-0.2679-0.0482-0.039-0.12580.19050.10940.2382-0.0609-0.04980.45190.09270.3809-33.4534-36.8292-19.9843
124.9817-0.56620.70281.6922-0.06621.8155-0.1548-0.36560.18990.09750.05290.0691-0.1246-0.34520.0730.24180.0251-0.00620.29770.01920.2597-17.41350.1006-4.2899
133.72050.65551.02552.64210.91851.87210.1823-0.2733-0.4650.186-0.0331-0.16550.27250.0971-0.12890.21290.0248-0.00760.25730.08040.31714.8772-12.3612-1.3818
143.4215-3.21990.288.0859-2.50994.11870.1315-0.2782-0.404-0.1796-0.38460.18950.3987-0.39620.01370.1379-0.26460.04190.38320.11760.2674-14.2878-15.2845-7.2856
155.5283-0.3910.4831.1881-0.04310.99310.0595-0.72810.36250.18330.04570.22970.0109-0.3456-0.07860.2909-0.04530.01380.659-0.02690.3859-52.1803-48.415412.2718
165.0150.20562.16762.21441.36933.70110.2758-0.7763-0.13010.13230.0244-0.19360.4166-0.0518-0.24690.2833-0.0352-0.05360.31790.00940.3399-26.9381-56.745213.7358
172.9796-1.7289-0.42744.013-0.52391.27670.2936-0.4424-0.78960.0426-0.09640.44780.5088-0.1808-0.21950.4512-0.2119-0.14590.47150.14370.4993-39.8552-68.501410.5881
184.4186-0.37360.37391.01150.35612.2181-0.20070.36580.8507-0.00690.1762-0.1024-0.38140.38660.0590.2933-0.0535-0.06720.43210.0970.397928.0545-41.704-40.6775
195.99131.14931.73723.3993-0.40343.8997-0.0607-0.09190.04160.21860.2194-0.42590.16490.1098-0.04910.237-0.0266-0.08210.5017-0.01680.357438.9461-50.7058-30.7014
204.21630.84711.49821.76350.72521.6401-0.0450.5061-0.0396-0.10080.088-0.0426-0.02120.2584-0.08950.2478-0.0326-0.03420.45540.06050.286325.6617-51.5199-40.0893
214.36241.17090.79774.7286-0.52662.5382-0.0302-0.25980.40660.14060.17790.3612-0.033-0.357-0.05920.26190.0283-0.06780.388-0.02110.255312.014-44.4088-31.4707
223.37331.6236-0.00884.1104-0.62142.9169-0.0634-0.05190.72740.33280.10290.2463-0.4977-0.422-0.08880.28620.1142-0.04430.3698-0.00120.4364.3718-39.6973-34.7198
234.5657-3.6205-1.43748.19313.48685.7167-0.46550.2350.6875-0.25970.0344-0.3365-0.9870.22040.11080.4424-0.2418-0.16030.440.25580.590123.7117-33.9955-41.0173
241.19490.64560.75180.63650.01880.79040.184-0.4882-0.47470.05640.15690.50830.008-0.7168-0.18990.33880.0861-0.12710.89120.12080.8132-43.5617-55.9141-60.1947
257.2284-1.36170.8673.2598-0.48412.84380.1502-0.7076-0.24150.77780.05411.115-0.5976-0.8662-0.07110.45280.20010.06120.84410.04250.7147-45.8755-46.1277-53.8013
263.017-0.5370.03212.2052-0.25352.42170.0410.15690.3963-0.0471-0.04630.3632-0.2836-0.35450.01180.31910.0928-0.09460.6150.04010.5943-36.2117-49.0158-61.6245
273.04711.66541.54553.36480.90943.08480.2011-0.0038-0.38970.0221-0.0278-0.24170.08470.1857-0.14240.20780.0277-0.02670.4980.11640.4137-17.4396-61.1315-55.4214
280.42380.36860.06341.16390.48181.6719-0.1042-0.03470.22170.2437-0.11760.45840.4167-0.20910.05410.3409-0.1461-0.06580.86270.17710.6385-32.4013-71.3174-54.8334
294.58040.20721.43820.82920.10391.2207-0.39950.40870.07230.08330.2896-0.1145-0.1051-0.38830.09350.3730.0271-0.14380.9692-0.21820.4773-55.5685-3.6247-53.0892
303.3010.8289-0.34462.6538-0.99710.8467-0.2455-0.5911-0.05880.18110.0724-0.13550.20530.26870.21160.45590.27980.01830.9251-0.08270.3513-79.9713-4.9357-46.9407
312.26190.70330.25261.9009-0.42091.0504-0.26180.15230.8390.36110.38140.3583-0.5356-0.5070.0070.46160.2162-0.20871.137-0.11110.6791-77.12687.8837-52.2433
322.8319-1.7207-1.04832.47860.16181.2173-0.3849-0.7386-0.02850.71920.31410.5906-0.2217-0.774-0.06780.56250.18240.13331.5789-0.03210.5915-10.0202-2.1715-72.638
332.6516-1.9527-1.23894.47541.55351.81180.2541-0.9390.5260.69040.25540.1233-0.6447-0.4726-0.30240.5690.26920.18521.46-0.16550.5183-6.71882.8796-74.6854
342.2236-1.2457-0.77613.0875-1.89582.47790.1175-1.09140.02120.6504-0.11890.2911-0.3593-0.863-0.23660.4629-0.0307-0.02971.1267-0.00980.37087.6315-8.2543-76.9117
352.69350.36114.6072.78150.99257.87370.0517-1.06360.03440.2495-0.2278-0.53380.27910.38430.1950.3165-0.0359-0.00811.15150.00470.458123.8912-10.3473-72.6865
362.5944-0.86840.19873.8585-0.2293.90750.2119-1.0649-0.96910.3873-0.19630.47680.8762-0.5651-0.05340.5184-0.23980.00091.04140.21140.64445.4456-22.9978-76.4061
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 116 )A25 - 116
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 178 )A117 - 178
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 212 )A179 - 212
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 249 )A213 - 249
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 271 )A250 - 271
7X-RAY DIFFRACTION7chain 'A' and (resid 272 through 350 )A272 - 350
8X-RAY DIFFRACTION8chain 'A' and (resid 351 through 370 )A351 - 370
9X-RAY DIFFRACTION9chain 'A' and (resid 371 through 392 )A371 - 392
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 177 )B4 - 177
11X-RAY DIFFRACTION11chain 'B' and (resid 178 through 392 )B178 - 392
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 212 )C1 - 212
13X-RAY DIFFRACTION13chain 'C' and (resid 213 through 370 )C213 - 370
14X-RAY DIFFRACTION14chain 'C' and (resid 371 through 392 )C371 - 392
15X-RAY DIFFRACTION15chain 'D' and (resid 4 through 212 )D4 - 212
16X-RAY DIFFRACTION16chain 'D' and (resid 213 through 316 )D213 - 316
17X-RAY DIFFRACTION17chain 'D' and (resid 317 through 392 )D317 - 392
18X-RAY DIFFRACTION18chain 'E' and (resid 3 through 59 )E3 - 59
19X-RAY DIFFRACTION19chain 'E' and (resid 60 through 116 )E60 - 116
20X-RAY DIFFRACTION20chain 'E' and (resid 117 through 212 )E117 - 212
21X-RAY DIFFRACTION21chain 'E' and (resid 213 through 249 )E213 - 249
22X-RAY DIFFRACTION22chain 'E' and (resid 250 through 370 )E250 - 370
23X-RAY DIFFRACTION23chain 'E' and (resid 371 through 392 )E371 - 392
24X-RAY DIFFRACTION24chain 'F' and (resid 3 through 50 )F3 - 50
25X-RAY DIFFRACTION25chain 'F' and (resid 51 through 116 )F51 - 116
26X-RAY DIFFRACTION26chain 'F' and (resid 117 through 212 )F117 - 212
27X-RAY DIFFRACTION27chain 'F' and (resid 213 through 316 )F213 - 316
28X-RAY DIFFRACTION28chain 'F' and (resid 317 through 392 )F317 - 392
29X-RAY DIFFRACTION29chain 'G' and (resid 6 through 212 )G6 - 212
30X-RAY DIFFRACTION30chain 'G' and (resid 213 through 271 )G213 - 271
31X-RAY DIFFRACTION31chain 'G' and (resid 272 through 392 )G272 - 392
32X-RAY DIFFRACTION32chain 'H' and (resid 7 through 116 )H7 - 116
33X-RAY DIFFRACTION33chain 'H' and (resid 117 through 178 )H117 - 178
34X-RAY DIFFRACTION34chain 'H' and (resid 179 through 249 )H179 - 249
35X-RAY DIFFRACTION35chain 'H' and (resid 250 through 296 )H250 - 296
36X-RAY DIFFRACTION36chain 'H' and (resid 297 through 391 )H297 - 391

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万見について

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お知らせ

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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

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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

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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

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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

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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。

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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