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- PDB-7szd: Crystal Structure Analysis of human PRPK complex with a compound -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7szd
タイトルCrystal Structure Analysis of human PRPK complex with a compound
要素
  • EKC/KEOPS complex subunit TP53RK
  • EKC/KEOPS complex subunit TPRKB
キーワードTRANSFERASE / protein kinase / p53 / immunomodulatory drugs / IMiDs
機能・相同性
機能・相同性情報


tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / 加水分解酵素; 酸無水物に作用 / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / 加水分解酵素; 酸無水物に作用 / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / hydrolase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Lipopolysaccharide kinase (Kdo/WaaP) family / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Chem-DVO / EKC/KEOPS complex subunit TP53RK / EKC/KEOPS complex subunit TPRKB
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: 2.05 Å
データ登録者Seo, H.-S. / Dhe-Paganon, S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: Biorxiv / 年: 2021
タイトル: Development of PRPK Directed Phthalimides
著者: Seo, H.-S. / Mizutani, T. / Hideshima, T. / Vangos, N.E. / Zhang, T. / Anderson, K.C. / Gray, N.S. / Dhe-Paganon, S.
履歴
登録2021年11月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月14日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年2月7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.pdbx_database_id_DOI / _citation.title / _citation.year

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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: EKC/KEOPS complex subunit TP53RK
B: EKC/KEOPS complex subunit TPRKB
C: EKC/KEOPS complex subunit TP53RK
D: EKC/KEOPS complex subunit TPRKB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,3026
ポリマ－96,6704
非ポリマー6332
水86548
1
A: EKC/KEOPS complex subunit TP53RK
B: EKC/KEOPS complex subunit TPRKB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,6513
ポリマ－48,3352
非ポリマー3161
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area18420 Å2
手法PISA
2
C: EKC/KEOPS complex subunit TP53RK
D: EKC/KEOPS complex subunit TPRKB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,6513
ポリマ－48,3352
非ポリマー3161
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-15 kcal/mol
Surface area18760 Å2
手法PISA
単位格子
Length a, b, c (Å)65.578, 79.038, 100.889
Angle α, β, γ (deg.)90.000, 105.614, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 18 through 77 or resid 79...A18 - 76
121(chain 'A' and (resid 18 through 77 or resid 79...A79 - 142
131(chain 'A' and (resid 18 through 77 or resid 79...A145 - 192
141(chain 'A' and (resid 18 through 77 or resid 79...A195 - 248
211(chain 'C' and (resid 18 through 68 or (resid 69...C18 - 76
221(chain 'C' and (resid 18 through 68 or (resid 69...C79 - 142
231(chain 'C' and (resid 18 through 68 or (resid 69...C145 - 192
241(chain 'C' and (resid 18 through 68 or (resid 69...C195 - 248
112(chain 'B' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))B0 - 12
122(chain 'B' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))B15 - 69
132(chain 'B' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))B72 - 174
142(chain 'B' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))B4000
212(chain 'D' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))D0 - 12
222(chain 'D' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))D15 - 69
232(chain 'D' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))D72 - 174
242(chain 'D' and (resid 0 through 13 or resid 15 through 70 or resid 72 through 4000))D4000

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 EKC/KEOPS complex subunit TP53RK / Atypical serine/threonine protein kinase TP53RK / Nori-2 / TP53-regulating kinase / p53-related protein kinase


分子量: 28358.646 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TP53RK, C20orf64, PRPK / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q96S44, 加水分解酵素; 酸無水物に作用, non-specific serine/threonine protein kinase
#2: タンパク質 EKC/KEOPS complex subunit TPRKB / PRPK-binding protein / TP53RK-binding protein


分子量: 19976.223 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TPRKB, CGI-121, My019 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9Y3C4
#3: 化合物 ChemComp-DVO / 2-[(3R)-3-methyl-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid


分子量: 316.266 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C15H12N2O6 / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 48 / 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

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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: 2.61 Å3/Da / 溶媒含有率: 52.8 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 100mM HEPES pH 7.5, 12% PEG 5000 MME, 10mM TCEP

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年2月16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: 0.9792 Å / 相対比: 1
反射解像度: 2.05→97.17 Å / Num. obs: 28212 / % possible obs: 89.9 % / 冗長度: 3.4 % / Biso Wilson estimate: 46.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Net I/σ(I): 10.3
反射 シェル解像度: 2.05→2.12 Å / Num. unique obs: 80 / CC1/2: 0.226

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHENIX1.17.1_3660精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
PDB_EXTRACT3.27データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 3ENP, 4WW5

3enp

4ww5


解像度: 2.05→97.17 Å / SU ML: 0.2782 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 41.485
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2754 1366 4.85 %
Rwork0.2207 26807 -
obs0.2233 28173 44.86 %
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 mean: 52.16 Å2
精密化ステップサイクル: LAST / 解像度: 2.05→97.17 Å
タンパク質核酸リガンド溶媒全体
原子数6267 0 0 48 6315
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01036362
X-RAY DIFFRACTIONf_angle_d1.4768618
X-RAY DIFFRACTIONf_chiral_restr0.07571026
X-RAY DIFFRACTIONf_plane_restr0.00861105
X-RAY DIFFRACTIONf_dihedral_angle_d13.5053920
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.226640.584680X-RAY DIFFRACTION1.34
2.12-2.20.3524100.3904265X-RAY DIFFRACTION4.44
2.2-2.30.4325270.3575496X-RAY DIFFRACTION8.43
2.3-2.430.3778410.3571851X-RAY DIFFRACTION14.22
2.43-2.580.4452630.3581364X-RAY DIFFRACTION22.92
2.58-2.780.39951310.33962141X-RAY DIFFRACTION36.16
2.78-3.060.33142320.31394095X-RAY DIFFRACTION68.77
3.06-3.50.32992660.26835815X-RAY DIFFRACTION97.11
3.5-4.410.26663190.19455777X-RAY DIFFRACTION96.38
4.41-97.170.21772730.17395923X-RAY DIFFRACTION96.54
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)
11.44712707807-0.3550132736891.275389431461.13570803082-0.843485034273.04207538570.6098320203260.411239411207-0.0631116493136-0.249349807230.261098837655-0.111069198407-0.7077169415380.3047015039490.9171285018390.349453993753-0.06659255415920.1868841961810.927931572054-0.1188476803090.60484273595731.57017217-1.656212665943.1863545962
21.78633833220.162370744290.507876723143.035488776890.08175605731541.51024969195-0.08487424098080.466108232037-0.241740520222-0.5125396051330.139691788223-0.8674449268840.1925372997821.06433106299-0.03121973875550.304414747535-0.0133200800876-0.08559980207030.5549490975520.018403693140.50459301362322.2040278716-9.4626416251636.5063732494
34.88556658661-1.855231935731.445721378812.422447958140.8186949366081.53241334214-0.028080231740.8899121242750.796124368309-0.6297707604820.179072090231-0.470022495281-0.3186634367070.4987197312580.5555022493040.301988269393-0.210702054242-0.05124596713120.279989505284-0.1286016921660.37780014818515.24810727142.7915007773232.9596843468
40.173577182089-0.1633582207060.2151035601710.154703735768-0.08357843840531.337882883050.147200249547-0.2835393115590.1765409302440.0417396890749-0.1582349283620.0685936511913-0.0006580859878620.265375960201-0.02352751805010.201575333505-0.09959969765460.01018001271820.252061462177-0.01373792924840.27667693589812.5052675114-6.1389906164540.8279323893
56.019255062721.023429340290.2880007020390.799175985640.3449710427052.82365949344-0.2356304220390.850529385298-0.899547421622-0.588376690403-0.209045522858-0.745701418221.40151875930.547547028744-0.2005249859590.8862086441230.00339132409056-0.1523176237470.3125400036270.04564000298150.5493690201472.9631151318-26.396248140525.4846283715
62.050694902310.903965777893-0.308168784160.431257640558-0.3823174187131.768932163480.0274900488082-0.273604519753-0.2591079778120.229243172536-0.1500953056820.709495288182-0.0427043623555-0.458875714594-1.24469398558-0.130161456578-0.537233264540.18862783516-0.1164063232610.08480744833150.29235998692-0.462674413701-11.987384631930.8003070732
70.648866509133-0.0805808855044-0.3095596454421.841697648490.2360530600840.2534150026-0.04239535042530.0312088874760.330550041943-0.4439854909780.05746994591760.169274922716-0.3193542623580.07806866737111.28046191340.433474144252-0.115867922639-0.1148815283550.0364457478572-0.1885873397860.2045588745336.824156357130.31224229550527.9338231933
80.503761770018-0.257013618648-0.03153998428771.78039857858-0.5464494176311.096643629020.2548831994240.255259858953-0.29387928221-0.5015417477250.01713233118930.9407465708140.336603265132-0.5015669623310.2602571111140.2980248904850.00466431186655-0.05171699536320.172086944777-0.05214229676550.377270012986-1.12025205827-10.937231703819.537752564
90.30026552373-0.0660069207878-0.06301504921921.535103261080.7279209255420.8434112078760.288743268892-0.297934323121.12464894402-0.4531806255480.2477032108750.290936460095-0.698577384902-0.344983987618-0.1825597797880.5690428393940.208305363142-0.01621704828050.444554317201-0.04093630592070.661056971031-4.26407404891-1.1044052566315.2185827388
100.008785357218220.121079196047-0.02085711206883.03362816552-0.4964728468160.07935161556040.615661500092-0.156884772288-0.2829137422551.164009607430.3237631549520.1776437732950.309321922813-0.3627953721430.3693430105220.6630428008150.0369216458164-0.1564443417110.641480058291-0.0169813878470.59531770087622.629881885-6.0498876345260.2446298254
110.308556917113-0.1082565921630.305212271940.296731952190.01636766841410.4021239993360.263935866719-0.2417289050020.5355766153730.879236393948-0.252520990285-0.2173793070710.121492627345-0.1462656715290.00175367849860.640321566059-0.2898151029430.07717759468440.616113582935-0.03481346873780.6109994130515.49656506827.1129204542970.0482170041
121.99417787701-1.21764873386-0.9012068314411.841995404430.03067066128610.6511004050360.0432586873437-0.5781071683650.125003718177-0.0341511734315-0.189523910141-0.384242666995-0.07716548878530.4330059291550.1708217483290.356576085819-0.2498183966740.02876909878180.5166838223160.07888472773090.19145698150612.39957297695.5798727380564.2636087722
130.3930481912560.459620482977-0.1603467854431.21623912681-0.2740194515350.920773969018-0.1429722917660.331750326138-0.0656247643535-0.1686846649630.133745955389-0.515557077865-0.3893884392920.566544568504-0.2891348171690.0346251193267-0.3564088052220.00230579837380.277668725976-0.05697196483510.24544843275819.57566134291.8932361931553.1717568353
141.178832078951.10497567779-0.2058197535841.35082045331-0.2991030157160.07038976655510.05774914589810.2964682926011.151452050080.169218875386-0.2117282517120.194127864768-0.6980849040661.02440836592-0.08971959367230.385011332041-0.171518328002-0.007068730323050.5212984659040.01836383051590.41433919962219.833152511410.973931408553.8672395595
152.45201441350.129643163019-0.2166178825271.864920801561.244553960443.331940291450.520470056251-0.18161039921.50878186943-1.14172842538-0.2487137537140.772811730822-0.848687334381-0.50581927566-0.004636839763730.615100457178-0.0893055219660.1321636331440.332589709071-0.06080890847930.4810907297139.2675001252213.984699756853.5758846066
162.255456861980.09407026255080.02646998557130.792655188241-0.2522918695611.078374161470.57752140443-1.258619703960.3761318783890.306555138339-0.01947868922130.0604113155233-0.278992060235-0.00574538324670.07760130947880.56660158783-0.3004569861940.02454184760520.591384006111-0.03509642837150.33736929720914.28215445186.1797621789566.0978488705
170.221293173958-0.06320209188040.07243525380460.0533284661058-0.06153775065230.06754428620320.225063540699-0.513090075469-0.133843641710.529019839384-0.0411472606699-0.635148837090.1345919990440.3771533988450.006955428412020.700831027615-0.15559055423-0.1133004566140.7064234845-0.008795723260620.62327338463625.36401721623.2071001697272.957520059
182.67001481478-0.389530273510.8840272251632.089622474960.177260913790.338118778707-0.0606168208181-0.833925468424-0.3409144318761.27704704274-0.21181725057-0.1294090359930.161144585776-0.651120182707-0.09728260680650.898978000157-0.3611592929590.0462438307610.7599560740540.07416920702580.4388374883367.59737144742-1.6909401537571.038521296
191.47523593975-0.3622851584890.8190000595881.96468772202-1.378934857821.77275374334-0.155355608758-0.6778826266870.4821689151250.780704206645-0.1278507857010.124969332077-0.405625261453-0.103757059998-0.3338458427110.369687117139-0.1082036580290.1000807073970.559415579404-0.0410906859320.471934766948-1.119385827654.2105414529356.3605750585
201.607389678590.8613503299150.8456423860850.581432263490.203473979462.51495907488-0.1930346301620.7524735441520.135656888952-0.134965042540.3653697233210.316444212743-0.0974704917127-0.5935557553480.4421180478220.228121257728-0.196729396989-0.04542931291150.488973848966-0.04432970098820.2966508705923.950248591520.46661464684746.8441093423
210.871380054395-0.3576300927840.195295961931.514228721.385777698772.17200782687-0.0459700787241-0.22006389173-0.4622333469220.4627049772370.2505397462430.1624286161631.56255218036-0.515339999260.1837541538881.11630140752-0.149737517542-0.04659062591260.354981799690.08916243978640.61490597097-23.2811777794-20.647198589493.0275815263
220.5264195014170.2336892054740.3762619476930.895450699106-0.3953822663121.661731334020.36367595556-0.08922875340350.0562351493571-0.220499105422-0.04016302785670.208015479248-0.00945334259696-0.2116108821460.5839300300830.397180872511-0.144005373236-0.01043199833740.3867112377450.1571277291980.414811539476-22.062138701-6.0568312794394.4517303714
231.691979101730.9474567366030.3723395188242.675224246391.338098235035.09501406062-0.0278766100083-0.166703241175-0.2023504474870.1219870397430.264182024164-0.6455660124180.8068911084081.620427197690.3454138751330.5084069945080.06291044727340.02070073757920.6319038832770.1456693422490.442166991862-5.73738119575-8.5321796480499.6917609565
240.823046149916-0.727928746739-0.7125236374010.7747322039520.2269902543632.421366574070.0275593904323-0.5506050219080.2248210593950.3517852766520.361400131795-0.271976890081-0.4066667075531.512060971670.2054741551620.654222895522-0.163552472612-0.009699822669461.001873145870.06941141480890.664759751427-1.772367483312.49646716164110.221350222
253.305518700040.06250094386761.896262544780.4062283984940.5899793587521.845752515080.7223108071740.917577224148-0.912393051754-0.494846621165-0.203147565176-0.4154003626040.204921915590.7724051029930.1493854538261.183217075060.11043014217-0.1021708493770.602648111103-0.1209008209820.703757258868-18.9092406148-24.854352825471.8937702373
261.504378310530.4484925324330.3733371774090.3317572873740.2141530262861.01831522393-0.197268047231.24783936595-0.213877627969-0.6570069349580.8136425019790.1698517030980.4002728041090.8591903502790.427900801140.810807037164-0.06568252920090.08643015838651.01183661621-0.1440905272520.637248991472-16.7826965065-17.610828074859.4030869838
270.142200964876-0.06517484137850.01948743039760.3575693601150.05153249834050.1905536988980.4414573597170.569159231824-0.154239409919-0.403808719552-0.2120442550390.2220787309-0.1471322293620.5452005208750.00200295481540.762559125840.04230157648530.06295247436980.8132682072310.005457632366770.559695787271-20.7614582709-10.235394267660.052874846
283.70941664956-0.04751261586132.872659102420.522920003113-0.96647410813.896176379750.2313839897030.357465370832-0.5631002720840.00296875957519-0.2381652859730.127833269550.89656371350.1323302132020.2894472699530.624630390753-0.08431456218040.002912312131210.2402288004190.02810321639190.359635122196-22.3703323514-15.122312910775.7554805552
290.5599609369430.398422920517-0.2929396871742.287347988080.186243505960.229136316333-0.133680832810.1310817748760.123550429081-0.005674127151290.0005276094851880.273337830880.305570635633-0.117211966915-1.370838861990.307023165209-0.2803146597330.006461402536320.3634159251120.3630590215830.395494998866-28.1134760964-8.9059300909372.2669287387
303.7424051766-0.4012041559914.178856180162.355845092881.094732736185.7135143135-0.03376688132380.8372854238780.0650874295065-0.5518743130490.0530376719221-0.31403529325-0.3303260728141.109374172840.8154537423110.399177847142-0.1482864703410.08495704928970.5377635855060.1916273512030.565619995651-19.0704572804-2.5724737500765.1873656951
310.211455895657-0.00251300996931-0.1700933146140.111682404995-0.001678058378920.154879914922-0.742897811340.499004449567-0.790117297822-0.4917562176210.134129979496-0.07616699693460.371355106556-0.1914918684610.000225098851030.827188997472-0.0368661471970.1317790236270.755157093593-0.06454816160010.685803178491-24.7406137312-21.749818357264.0604207181
320.168518976341-0.03199281042710.2131147940413.52757667059-0.9738472792630.518968030056-0.4345174862420.793960868709-0.913739830637-1.006854292570.391509150705-0.1974397136830.6338841871440.4451137070110.1211112045960.7951774255020.1396828922050.1109679189871.56231232073-0.1532974374840.734548634886-15.3876035864-19.665545654855.2784156768
330.694703395264-0.180298803937-0.06179822175330.26234065897-0.3494787933750.6277680106320.1535424696691.286103966990.253512315686-0.326590696574-0.530429575786-0.21090547151-0.1481139766670.321752626024-0.1889378241410.419718740086-0.1275186583510.1648786073071.249849764570.1471300470770.931954820402-6.12547944079-4.796511910167.9397379249
340.0893091085198-0.1013574574140.04668257129680.4277580656230.02922465901060.2762349339610.06453292127580.006059398390420.1973771224440.629086184247-0.0840525764112-0.000868208769558-0.437950820821.27662659658-0.006621491062570.7278527362910.04025870591230.06536432535480.8913929744130.1653819831790.86022755649-3.30273544044-2.3860830018881.3075749481
351.90543277222-1.97806338211-1.511031392322.687599455393.658283206018.166842665490.110171863638-0.03223577455620.8959624667480.4188220672050.188280809791-0.2787597114820.03808895636171.221149713650.7579927690060.266201947091-0.02960369904640.00700981314530.351283475740.1706680351630.546758709005-14.654436891-6.4007676688980.5359471719
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 121 )
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 181 )
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 228 )
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 12 )
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 35 )
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 50 )
13X-RAY DIFFRACTION13chain 'B' and (resid 51 through 66 )
14X-RAY DIFFRACTION14chain 'B' and (resid 67 through 83 )
15X-RAY DIFFRACTION15chain 'B' and (resid 84 through 95 )
16X-RAY DIFFRACTION16chain 'B' and (resid 96 through 112 )
17X-RAY DIFFRACTION17chain 'B' and (resid 113 through 125 )
18X-RAY DIFFRACTION18chain 'B' and (resid 126 through 141 )
19X-RAY DIFFRACTION19chain 'B' and (resid 142 through 149 )
20X-RAY DIFFRACTION20chain 'B' and (resid 150 through 175 )
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 69 )
22X-RAY DIFFRACTION22chain 'C' and (resid 70 through 92 )
23X-RAY DIFFRACTION23chain 'C' and (resid 93 through 210 )
24X-RAY DIFFRACTION24chain 'C' and (resid 211 through 249 )
25X-RAY DIFFRACTION25chain 'D' and (resid 0 through 12 )
26X-RAY DIFFRACTION26chain 'D' and (resid 13 through 25 )
27X-RAY DIFFRACTION27chain 'D' and (resid 26 through 50 )
28X-RAY DIFFRACTION28chain 'D' and (resid 51 through 66 )
29X-RAY DIFFRACTION29chain 'D' and (resid 67 through 83 )
30X-RAY DIFFRACTION30chain 'D' and (resid 84 through 104 )
31X-RAY DIFFRACTION31chain 'D' and (resid 105 through 118 )
32X-RAY DIFFRACTION32chain 'D' and (resid 119 through 136 )
33X-RAY DIFFRACTION33chain 'D' and (resid 137 through 149 )
34X-RAY DIFFRACTION34chain 'D' and (resid 150 through 160 )
35X-RAY DIFFRACTION35chain 'D' and (resid 161 through 175 )

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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