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万見
- PDB-4r7n: Fab C2E3 -

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データを開く


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: 4r7n
タイトルFab C2E3
要素
  • Fab C2E3 Heavy chain
  • Fab C2E3 Light chain
キーワードIMMUNE SYSTEM / TLR4 antibody
機能・相同性Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
機能・相同性情報
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: 3.45 Å
データ登録者Loyau, J. / Didelot, G. / Malinge, P. / Ravn, U. / Magistrelli, G. / Depoisier, J.F. / Kosco-Vilbois, M. / Fischer, N. / Thore, S. / Rousseau, F.
引用ジャーナル: J.Mol.Biol. / 年: 2015
タイトル: Robust Antibody-Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking.
著者: Loyau, J. / Didelot, G. / Malinge, P. / Ravn, U. / Magistrelli, G. / Depoisier, J.F. / Pontini, G. / Poitevin, Y. / Kosco-Vilbois, M. / Fischer, N. / Thore, S. / Rousseau, F.
履歴
登録2014年8月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年7月29日Provider: repository / タイプ: Initial release
改定 1.12015年8月26日Group: Database references
改定 1.22024年11月20日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Fab C2E3 Heavy chain
B: Fab C2E3 Light chain
C: Fab C2E3 Heavy chain
D: Fab C2E3 Light chain
E: Fab C2E3 Heavy chain
F: Fab C2E3 Light chain
G: Fab C2E3 Heavy chain
H: Fab C2E3 Light chain
I: Fab C2E3 Heavy chain
J: Fab C2E3 Light chain
K: Fab C2E3 Heavy chain
L: Fab C2E3 Light chain
M: Fab C2E3 Heavy chain
N: Fab C2E3 Light chain
O: Fab C2E3 Heavy chain
P: Fab C2E3 Light chain
Q: Fab C2E3 Heavy chain
R: Fab C2E3 Light chain
S: Fab C2E3 Heavy chain
T: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)478,24420
ポリマ－478,24420
非ポリマー00
水00
1
A: Fab C2E3 Heavy chain
B: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area19680 Å2
手法PISA
2
C: Fab C2E3 Heavy chain
D: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area19660 Å2
手法PISA
3
E: Fab C2E3 Heavy chain
F: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-24 kcal/mol
Surface area19910 Å2
手法PISA
4
G: Fab C2E3 Heavy chain
H: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-24 kcal/mol
Surface area19680 Å2
手法PISA
5
I: Fab C2E3 Heavy chain
J: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-23 kcal/mol
Surface area19740 Å2
手法PISA
6
K: Fab C2E3 Heavy chain
L: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-25 kcal/mol
Surface area19860 Å2
手法PISA
7
M: Fab C2E3 Heavy chain
N: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-25 kcal/mol
Surface area19690 Å2
手法PISA
8
O: Fab C2E3 Heavy chain
P: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area20790 Å2
手法PISA
9
Q: Fab C2E3 Heavy chain
R: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area19800 Å2
手法PISA
10
S: Fab C2E3 Heavy chain
T: Fab C2E3 Light chain


分子量 (理論値)分子数
合計 (水以外)47,8242
ポリマ－47,8242
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-23 kcal/mol
Surface area19760 Å2
手法PISA
単位格子
Length a, b, c (Å)178.100, 208.410, 214.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
詳細heterodimer with assembly identifier 2 / heterodimer with assembly identifier 1

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要素

#1: 抗体
Fab C2E3 Heavy chain


分子量: 24305.307 Da / 分子数: 10 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): Ovary cells
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#2: 抗体
Fab C2E3 Light chain


分子量: 23519.068 Da / 分子数: 10 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): Ovary cells
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
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: 4.16 Å3/Da / 溶媒含有率: 70.43 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: 20% PEG 3350, 0.1M Bis Tris Propane pH 8.5, 0.23M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: X06DA / 波長: 0.99987 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2014年2月13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: 0.99987 Å / 相対比: 1
反射解像度: 3.45→50 Å / Num. all: 105492 / Num. obs: 105387 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
反射 シェル解像度: 3.45→3.54 Å / 冗長度: 7.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 7717 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
StructureStudioデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.1_1168)精密化
XDSデータ削減
XDSデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.45→48.775 Å / SU ML: 0.47 / σ(F): 1.35 / 位相誤差: 31.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.28 5001 4.75 %RANDOM
Rwork0.2358 ---
obs0.2379 105261 99.89 %-
all-105377 --
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
精密化ステップサイクル: LAST / 解像度: 3.45→48.775 Å
タンパク質核酸リガンド溶媒全体
原子数32933 0 0 0 32933
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00433832
X-RAY DIFFRACTIONf_angle_d0.8646041
X-RAY DIFFRACTIONf_dihedral_angle_d12.9412101
X-RAY DIFFRACTIONf_chiral_restr0.0545182
X-RAY DIFFRACTIONf_plane_restr0.0045865
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.4501-3.48930.38151720.331733293329
3.4893-3.53030.34341640.320732953295
3.5303-3.57330.36491650.325433073307
3.5733-3.61850.33921520.299632883288
3.6185-3.66610.32051750.291532983298
3.6661-3.71640.38581660.294933373337
3.7164-3.76940.36841630.301432843884
3.7694-3.82570.35941660.286233223322
3.8257-3.88540.35341650.27932823282
3.8854-3.94910.29491680.268433253325
3.9491-4.01720.2831530.258232913291
4.0172-4.09020.28111680.258233323332
4.0902-4.16880.31221710.250933173317
4.1688-4.25380.28731610.234233283328
4.2538-4.34630.28111750.227633373337
4.3463-4.44730.27231630.207832993299
4.4473-4.55850.24961660.203333473347
4.5585-4.68160.25511600.20633253325
4.6816-4.81930.2371720.197433403340
4.8193-4.97470.23331590.192733443344
4.9747-5.15230.22651710.233183318
5.1523-5.35830.2471610.198133733373
5.3583-5.60190.25781670.206833393339
5.6019-5.89670.25881760.209533473347
5.8967-6.26550.24181640.215333603360
6.2655-6.74810.29881700.239533723372
6.7481-7.42510.27281720.240234193419
7.4251-8.49460.25191610.221434003400
8.4946-10.68370.23141730.200634303430
10.6837-48.77970.31841820.272635753575
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)
11.23960.4980.86060.62780.59871.43660.1476-0.1871-0.2975-0.1517-0.07570.028-0.07330.320200.6574-0.0090.11720.62020.07480.7415202.2189215.4853488.7245
20.8656-0.0428-0.1435-0.4220.8855-0.67510.00690.0521-0.163-0.0967-0.0758-0.0959-0.1929-0.080600.91370.04250.09810.90080.14150.8929184.4705227.2447479.4961
30.62410.1716-0.3507-0.007-1.0113-0.21280.05330.4103-0.01330.14480.11990.25450.0595-0.101-00.84160.1046-0.06490.77630.10970.9414177.0978230.1034473.4417
40.6738-0.65170.07090.7905-0.49540.63810.1642-0.52250.0156-0.30970.22070.2715-0.37780.234900.9555-0.09270.19520.8358-0.14460.7773203.6178238.9434496.481
50.38580.19560.14470.30290.2507-0.34990.59730.01940.28610.1182-0.34850.2133-0.03630.536301.09960.0770.07990.8602-0.16620.9688202.0078234.9738495.4888
60.683-0.3622-0.28680.45520.2597-0.38450.3159-0.11350.19-0.0555-0.3161-0.00620.08410.016200.87580.04540.05490.7529-0.051.1159171.4537238.6046484.7871
70.26480.0594-0.2950.11580.08631.20350.4322-0.13870.0976-0.0999-0.10130.1599-0.084-0.089100.8440.154-0.04930.8585-0.04721.1821165.6578237.7243485.6401
80.4177-0.0296-1.37210.23080.29490.60050.2838-0.30820.0581-0.10790.25340.3705-0.13680.2392-00.8364-0.0509-0.0921.0665-0.14531.1654121.8691304.7206479.5105
90.4151-0.2174-0.12110.47560.3143-0.0753-0.08790.6330.53550.53670.214-0.32960.0884-0.015-00.7786-0.0133-0.19590.8936-0.04611.1329121.7965305.9675474.9593
100.611-0.45040.10230.01910.18550.5245-0.3566-0.22240.21110.97030.5013-0.2779-0.0509-0.1665-01.07530.11810.08990.9450.17130.886995.4404289.7506490.6842
111.0851-0.4668-0.47690.1708-0.37460.0921-0.0660.1660.3449-0.08820.14950.07620.48070.187201.18550.07830.03520.75930.03760.955898.3111291.384491.2377
120.0687-0.2621-0.3724-0.0050.0024-0.2462-0.43661.1452-0.3167-0.28580.999-0.00760.6148-0.052101.00970.0615-0.21411.17340.01350.9874117.5889281.0417464.3422
130.10360.22660.37090.65450.06860.2060.31460.20590.10090.43770.22040.09620.22180.244900.98270.0661-0.12361.0643-0.15910.9046125.1333287.2831468.5386
140.1551-0.1380.07540.040.12680.142-0.040.7248-0.55160.17090.6635-0.17490.51630.946401.08660.1-0.14011.3061-0.43471.157131.1305281.0274475.1822
150.28370.05170.51280.2051-0.12120.0486-0.4419-0.12290.66230.42510.7176-0.31020.62020.17300.86680.1052-0.15190.9384-0.21771.1213123.3921280.4608469.0527
160.0111-0.0395-0.02110.06890.0004-0.07860.83020.2459-0.0746-0.780.1682-0.23380.48480.409600.677-0.1488-0.09040.8783-0.21550.8933127.9733296.2823463.8113
170.1739-0.00120.13520.0215-0.2688-0.09571.07190.18280.18140.685-0.57810.4369-0.21120.089900.7546-0.03280.03470.72520.04480.9373100.9358276.3499477.0182
18-0.0886-0.14230.01010.0296-0.20640.13980.13180.24160.720.3304-0.22430.54990.50030.539-01.1980.21970.20130.92840.07931.223884.8846292.6111487.5325
190.08720.19790.01290.33680.17460.00670.47850.6121-0.2621-0.018-0.03520.3230.9069-0.576200.9866-0.0038-0.02881.2421-0.0341.176292.1282279.6079475.006
200.0147-0.07090.01860.09460.16570.10170.4446-0.4640.32040.173-0.0161-0.1685-0.01-0.20800.8975-0.1430.06831.08110.10741.402283.9042287.6058474.482
210.03720.0667-0.10290.2166-0.14130.0134-0.08340.3284-0.00780.43630.07750.221-0.09710.308500.92880.0406-0.03030.93890.05581.103894.2383285.7945480.2399
220.12110.07040.5342-0.24020.47640.38660.3725-0.3255-0.9674-0.15840.19390.16240.0611-0.146501.0749-0.02440.29471.27270.04981.68681.853279.3091480.3163
230.0457-0.0736-0.04380.18310.14910.04-0.5004-0.3060.5921-0.045-0.0196-0.2031-0.0227-0.081201.2512-0.21760.28711.755-0.59031.018293.5411253.2488447.3525
24-0.18260.0598-0.10670.2569-0.1769-0.0123-0.45960.2565-0.03140.29230.28670.8313-0.08050.8122-01.1969-0.18270.1661.4222-0.36181.1193103.6242250.5035448.0055
250.50570.1002-0.02670.29210.01010.0543-0.56230.0581-0.65550.0977-0.00430.0399-0.25050.011701.5076-0.38890.35031.5413-0.38621.2653100.3861244.5349451.7859
260.0463-0.0227-0.21490.15510.062-0.0283-0.38441.2489-0.74630.1184-0.30670.29340.3772-0.5876-00.9898-0.2010.00421.4637-0.26020.7628107.8964255.3749446.7911
270.3186-0.3676-1.3288-0.01950.3450.925-0.36710.6075-0.2133-0.3660.12760.51480.2459-0.328601.1924-0.2124-0.12551.85-0.58771.392481.3432270.6232448.7712
280.1107-0.1875-0.10330.0360.07040.1341-0.48430.3660.65090.0888-1.08851.0757-0.8344-0.53201.3895-0.2407-1.13264.45240.14910.100684.2952286.8281442.3701
29-0.09430.06630.08580.0736-0.1459-0.0433-0.38031.0645-0.93470.20370.83631.27971.12290.297401.2383-0.1085-0.27352.4597-0.55191.50785.9661268.7075444.4614
30-0.1149-0.1576-0.2267-0.0428-0.13-0.081-0.2244-0.33380.48850.2079-0.5380.3728-0.90210.0371-01.1017-0.2327-0.23761.88320.06211.03787.4193273.9718449.4594
310.0937-0.06570.4405-0.1605-0.0514-0.3041-1.28841.6681-2.0852-0.6351-1.4638-1.14551.3264-0.1921-0-3.1565-0.4439-4.42212.96950.1924-3.100683.3229276.4214437.6397
320.6157-0.01920.19560.96931.18580.0837-0.30850.29130.17950.30890.34440.18040.19860.241801.0011-0.0027-0.04370.9925-0.11570.6799116.1052266.4911453.998
33-0.19490.4063-0.21550.3832-0.3914-0.2918-0.10550.15650.2988-0.01230.26040.26470.20640.281801.1690.0055-0.00621.1639-0.16110.9677113.7242270.0092454.5749
340.071-0.3625-0.03320.19640.61080.11120.07771.290.47660.54690.09120.1172-0.20.0887-00.93860.1624-0.14581.75150.23291.354683.3847285.3662452.5563
350.2156-0.15960.05070.0107-0.89640.22270.06680.64420.29480.27420.28640.18990.1082-0.259300.82370.1261-0.11921.47330.28821.351884.1733287.8034455.4632
360.824-0.24740.41310.78520.06470.2270.104-0.2494-0.0883-0.2085-0.1553-0.2442-0.0781-0.1266-00.7391-0.00810.02180.86940.12660.8917157.6405203.1847489.556
370.6202-0.1466-0.29320.1006-0.09690.3978-0.0713-0.16550.1259-0.0510.06480.0902-0.13740.1223-00.9557-0.015-0.08150.90460.00950.9012135.9902215.7732501.0638
380.40630.0296-0.37870.10490.29390.63770.1332-0.1129-0.14090.0239-0.1936-0.3718-0.0181-0.2174-00.8527-0.0313-0.09620.81770.21320.8476157.1522195.3894511.6564
390.55940.0137-0.3585-0.1420.48070.5054-0.0846-0.15040.13460.0690.1034-0.00450.1493-0.2006-01.0612-0.0071-0.081.28730.05180.7298127.6641209.1767511.0766
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710.1088-0.4672-0.44890.1879-0.2374-0.4982-0.69391.1422-1.09981.09292.056-0.558-0.05251.046101.3774-0.10870.48791.20621.06681.0996142.5054282.3896546.0923
720.18650.98790.00510.34240.3410.2963-0.45520.1086-0.31780.06090.4062-0.3734-0.2385-0.3641-01.21210.16680.20811.27370.4291.1013142.0051285.304547.5309
730.01490.21230.0025-0.16080.2266-0.07051.477-0.0314-0.411-0.3794-1.6987-0.71760.20110.52203.5901-0.7125-0.08942.0281-0.21992.6882122.2031275.8379509.0076
740.3860.52550.46780.05330.347-0.0406-0.5735-0.0526-0.32130.44870.2679-0.0750.7969-0.737802.3114-0.56450.20371.78010.42522.2479126.3183277.0656523.1372
750.3890.1449-0.11370.4633-0.11870.7026-0.2388-0.1550.1325-0.32130.2602-0.32850.2436-0.5608-01.4699-0.23040.19410.99940.19621.0263157.796287.8426530.7076
76-0.05650.0830.00320.29440.61180.0254-1.83780.3630.57840.33661.30811.51341.56832.128900.7954-1.5322-0.58980.83830.88722.0111127.9607288.466509.1197
770.4042-0.12540.4750.3101-0.15230.2527-0.22520.00290.4355-0.0367-0.05880.22150.0710.1296-01.06390.132-0.13790.9264-0.10341.5922138.9884255.2983496.3692
781.54520.3233-0.09210.59020.47270.0448-0.04750.00950.12090.03380.15310.05290.1842-0.066301.04530.0787-0.04761.02520.09981.0757131.9633228.1741479.7442
790.02820.262-0.16930.0821-0.1383-0.0835-0.57631.01981.37530.18580.37440.110.0874-0.1165-01.55490.0338-0.56951.56960.36562.3782135.709261.6263469.4971
800.12580.0428-0.04210.0547-0.0099-0.01940.38510.76560.2851-0.08730.2708-0.4044-0.3399-0.899-01.94280.0419-0.4711.51630.0352.5879139.9952271.6303476.2008
810.0349-0.02120.24050.0249-0.0322-0.1177-2.2350.7590.59840.27-0.50370.20561.4077-0.806301.0890.2598-0.66230.90930.56571.8996142.023255.6593479.3635
820.0520.0164-0.00910.0407-0.07860.0612-0.72660.0058-0.07910.3819-0.59710.6647-0.87060.758401.5921-0.2232-0.13731.32730.33912.0123151.0465260.8126474.9165
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850.047-0.06990.01020.05240.02950.25630.34960.64250.26420.5634-0.2312-0.26580.3040.245701.2238-0.0035-0.02261.21910.27891.2388131.648241.3222464.0649
86-0.06160.04060.21730.24970.49770.75030.1708-0.02750.2259-0.2013-0.15090.0924-0.0687-0.4934-00.93570.0737-0.03531.37860.31921.1801119.7706230.923470.8456
870.2052-0.13640.3840.0525-0.24240.5020.3269-0.70270.20430.0458-0.70210.4462-0.31450.511801.22120.0962-0.21471.40820.08171.4588123.5217236.0395472.792
880.0719-0.10550.03440.07140.0441-0.00920.0113-0.1757-0.52720.01710.33290.212-0.9836-0.525501.3445-0.1975-0.07121.41960.32031.401113.2211225.8401467.5501
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920.28340.1848-0.30280.0548-0.1582-0.0816-0.175-1.34950.2997-1.7092-1.43920.3410.27740.073302.20750.7445-1.45151.4811-1.31112.895149.0245365.547498.439
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1000.17180.4174-0.07060.1243-0.51860.1105-0.02320.68161.0305-1.59250.48831.00650.8570.327803.1975-0.0078-1.39532.0380.26912.8708155.566367.0946475.7111
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104-0.14670.13510.0338-0.0538-0.1104-0.0847-1.28430.12120.0325-0.083-1.10190.3443-0.3725-0.7922-02.3589-0.5734-0.5593.0076-0.35871.5101130.8512335.7407460.6117
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 218 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 75 )
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 211 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 45 )
9X-RAY DIFFRACTION9chain 'C' and (resid 46 through 124 )
10X-RAY DIFFRACTION10chain 'C' and (resid 125 through 162 )
11X-RAY DIFFRACTION11chain 'C' and (resid 163 through 218 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 18 )
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 49 )
14X-RAY DIFFRACTION14chain 'D' and (resid 50 through 61 )
15X-RAY DIFFRACTION15chain 'D' and (resid 62 through 89 )
16X-RAY DIFFRACTION16chain 'D' and (resid 90 through 101 )
17X-RAY DIFFRACTION17chain 'D' and (resid 102 through 118 )
18X-RAY DIFFRACTION18chain 'D' and (resid 119 through 136 )
19X-RAY DIFFRACTION19chain 'D' and (resid 137 through 150 )
20X-RAY DIFFRACTION20chain 'D' and (resid 151 through 163 )
21X-RAY DIFFRACTION21chain 'D' and (resid 164 through 186 )
22X-RAY DIFFRACTION22chain 'D' and (resid 187 through 211 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 16 )
24X-RAY DIFFRACTION24chain 'E' and (resid 17 through 52 )
25X-RAY DIFFRACTION25chain 'E' and (resid 53 through 91 )
26X-RAY DIFFRACTION26chain 'E' and (resid 92 through 111 )
27X-RAY DIFFRACTION27chain 'E' and (resid 112 through 134 )
28X-RAY DIFFRACTION28chain 'E' and (resid 135 through 148 )
29X-RAY DIFFRACTION29chain 'E' and (resid 149 through 162 )
30X-RAY DIFFRACTION30chain 'E' and (resid 163 through 182 )
31X-RAY DIFFRACTION31chain 'E' and (resid 183 through 218 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 61 )
33X-RAY DIFFRACTION33chain 'F' and (resid 62 through 114 )
34X-RAY DIFFRACTION34chain 'F' and (resid 115 through 150 )
35X-RAY DIFFRACTION35chain 'F' and (resid 151 through 211 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 98 )
37X-RAY DIFFRACTION37chain 'G' and (resid 99 through 218 )
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 101 )
39X-RAY DIFFRACTION39chain 'H' and (resid 102 through 144 )
40X-RAY DIFFRACTION40chain 'H' and (resid 145 through 211 )
41X-RAY DIFFRACTION41chain 'I' and (resid 1 through 45 )
42X-RAY DIFFRACTION42chain 'I' and (resid 46 through 124 )
43X-RAY DIFFRACTION43chain 'I' and (resid 125 through 218 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 101 )
45X-RAY DIFFRACTION45chain 'J' and (resid 102 through 144 )
46X-RAY DIFFRACTION46chain 'J' and (resid 145 through 211 )
47X-RAY DIFFRACTION47chain 'K' and (resid 1 through 40 )
48X-RAY DIFFRACTION48chain 'K' and (resid 41 through 52 )
49X-RAY DIFFRACTION49chain 'K' and (resid 53 through 64 )
50X-RAY DIFFRACTION50chain 'K' and (resid 65 through 84 )
51X-RAY DIFFRACTION51chain 'K' and (resid 85 through 124 )
52X-RAY DIFFRACTION52chain 'K' and (resid 125 through 139 )
53X-RAY DIFFRACTION53chain 'K' and (resid 140 through 162 )
54X-RAY DIFFRACTION54chain 'K' and (resid 163 through 196 )
55X-RAY DIFFRACTION55chain 'K' and (resid 197 through 218 )
56X-RAY DIFFRACTION56chain 'L' and (resid 1 through 75 )
57X-RAY DIFFRACTION57chain 'L' and (resid 76 through 113 )
58X-RAY DIFFRACTION58chain 'L' and (resid 114 through 155 )
59X-RAY DIFFRACTION59chain 'L' and (resid 156 through 211 )
60X-RAY DIFFRACTION60chain 'M' and (resid 1 through 34 )
61X-RAY DIFFRACTION61chain 'M' and (resid 35 through 98 )
62X-RAY DIFFRACTION62chain 'M' and (resid 99 through 182 )
63X-RAY DIFFRACTION63chain 'M' and (resid 183 through 218 )
64X-RAY DIFFRACTION64chain 'N' and (resid 1 through 33 )
65X-RAY DIFFRACTION65chain 'N' and (resid 34 through 75 )
66X-RAY DIFFRACTION66chain 'N' and (resid 76 through 101 )
67X-RAY DIFFRACTION67chain 'N' and (resid 102 through 128 )
68X-RAY DIFFRACTION68chain 'N' and (resid 129 through 155 )
69X-RAY DIFFRACTION69chain 'N' and (resid 156 through 174 )
70X-RAY DIFFRACTION70chain 'N' and (resid 175 through 211 )
71X-RAY DIFFRACTION71chain 'O' and (resid 1 through 52 )
72X-RAY DIFFRACTION72chain 'O' and (resid 53 through 124 )
73X-RAY DIFFRACTION73chain 'O' and (resid 125 through 141 )
74X-RAY DIFFRACTION74chain 'O' and (resid 142 through 218 )
75X-RAY DIFFRACTION75chain 'P' and (resid 1 through 102 )
76X-RAY DIFFRACTION76chain 'P' and (resid 103 through 211 )
77X-RAY DIFFRACTION77chain 'Q' and (resid 1 through 124 )
78X-RAY DIFFRACTION78chain 'Q' and (resid 125 through 218 )
79X-RAY DIFFRACTION79chain 'R' and (resid 1 through 18 )
80X-RAY DIFFRACTION80chain 'R' and (resid 19 through 32 )
81X-RAY DIFFRACTION81chain 'R' and (resid 33 through 44 )
82X-RAY DIFFRACTION82chain 'R' and (resid 45 through 64 )
83X-RAY DIFFRACTION83chain 'R' and (resid 65 through 90 )
84X-RAY DIFFRACTION84chain 'R' and (resid 91 through 101 )
85X-RAY DIFFRACTION85chain 'R' and (resid 102 through 118 )
86X-RAY DIFFRACTION86chain 'R' and (resid 119 through 155 )
87X-RAY DIFFRACTION87chain 'R' and (resid 156 through 186 )
88X-RAY DIFFRACTION88chain 'R' and (resid 187 through 197 )
89X-RAY DIFFRACTION89chain 'R' and (resid 198 through 213 )
90X-RAY DIFFRACTION90chain 'S' and (resid 1 through 16 )
91X-RAY DIFFRACTION91chain 'S' and (resid 17 through 34 )
92X-RAY DIFFRACTION92chain 'S' and (resid 35 through 76 )
93X-RAY DIFFRACTION93chain 'S' and (resid 77 through 98 )
94X-RAY DIFFRACTION94chain 'S' and (resid 99 through 111 )
95X-RAY DIFFRACTION95chain 'S' and (resid 112 through 139 )
96X-RAY DIFFRACTION96chain 'S' and (resid 140 through 162 )
97X-RAY DIFFRACTION97chain 'S' and (resid 163 through 196 )
98X-RAY DIFFRACTION98chain 'S' and (resid 197 through 218 )
99X-RAY DIFFRACTION99chain 'T' and (resid 1 through 25 )
100X-RAY DIFFRACTION100chain 'T' and (resid 26 through 90 )
101X-RAY DIFFRACTION101chain 'T' and (resid 91 through 136 )
102X-RAY DIFFRACTION102chain 'T' and (resid 137 through 163 )
103X-RAY DIFFRACTION103chain 'T' and (resid 164 through 197 )
104X-RAY DIFFRACTION104chain 'T' and (resid 198 through 211 )

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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