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- PDB-3auv: Predicting Amino Acid Preferences in the Complementarity Determin... -

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基本情報

登録情報
データベース: PDB / ID: 3auv
タイトルPredicting Amino Acid Preferences in the Complementarity Determining Regions of an Antibody-Antigen Recognition Interface
要素sc-dsFv derived from the G6-Fab
キーワードIMMUNE SYSTEM / sc-dsFv (disulfide-stabilized scFv) / scFv / monovalent antibody / VEGF / antibody engineering
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: 2.4 Å
データ登録者Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. ...Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. / Ma, A.C. / Yang, A.S.
引用ジャーナル: Plos One / 年: 2012
タイトル: Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface
著者: Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. / ...著者: Yu, C.M. / Peng, H.P. / Chen, I.C. / Lee, Y.C. / Chen, J.B. / Tsai, K.C. / Chen, C.T. / Chang, J.Y. / Yang, E.W. / Hsu, P.C. / Jian, J.W. / Hsu, H.J. / Chang, H.J. / Hsu, W.L. / Huang, K.F. / Ma, A.C. / Yang, A.S.
履歴
登録2011年2月16日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02012年2月22日Provider: repository / タイプ: Initial release
改定 1.12012年2月29日Group: Database references
改定 1.22012年4月25日Group: Database references
改定 1.32024年11月13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: sc-dsFv derived from the G6-Fab
B: sc-dsFv derived from the G6-Fab
C: sc-dsFv derived from the G6-Fab
D: sc-dsFv derived from the G6-Fab
E: sc-dsFv derived from the G6-Fab
F: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)174,9386
ポリマ－174,9386
非ポリマー00
水9,746541
1
A: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)29,1561
ポリマ－29,1561
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
A: sc-dsFv derived from the G6-Fab
C: sc-dsFv derived from the G6-Fab
E: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)87,4693
ポリマ－87,4693
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area25990 Å2
手法PISA
8
B: sc-dsFv derived from the G6-Fab
D: sc-dsFv derived from the G6-Fab
F: sc-dsFv derived from the G6-Fab


分子量 (理論値)分子数
合計 (水以外)87,4693
ポリマ－87,4693
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area26030 Å2
手法PISA
単位格子
Length a, b, c (Å)136.063, 136.063, 169.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 12:117 or resseq 136:253 )A12 - 117
121chain A and (resseq 12:117 or resseq 136:253 )A136 - 253
211chain B and (resseq 12:117 or resseq 136:253 )B12 - 117
221chain B and (resseq 12:117 or resseq 136:253 )B136 - 253
311chain C and (resseq 12:117 or resseq 136:253 )C12 - 117
321chain C and (resseq 12:117 or resseq 136:253 )C136 - 253
411chain D and (resseq 12:117 or resseq 136:253 )D12 - 117
421chain D and (resseq 12:117 or resseq 136:253 )D136 - 253
511chain E and (resseq 12:117 or resseq 136:253 )E12 - 117
521chain E and (resseq 12:117 or resseq 136:253 )E136 - 253
611chain F and (resseq 12:117 or resseq 136:253 )F12 - 117
621chain F and (resseq 12:117 or resseq 136:253 )F136 - 253

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要素

#1: 抗体
sc-dsFv derived from the G6-Fab


分子量: 29156.348 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 541 / 由来タイプ: 天然 / 式: H2O
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: 2.58 Å3/Da / 溶媒含有率: 52.35 %
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: 8
詳細: 100mM Tris-HCl, 100mM MgCl2, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: NSRRC / ビームライン: BL13C1 / 波長: 0.97622 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2010年10月7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: 0.97622 Å / 相対比: 1
反射解像度: 2.4→30 Å / Num. obs: 70426 / % possible obs: 99.1 % / 冗長度: 8.2 %
反射 シェル解像度: 2.4→2.49 Å / 冗長度: 7.7 % / Num. unique all: 6598 / % possible all: 93.9

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
MOLREP位相決定
PHENIX(phenix.refine: 1.7_648)精密化
HKL-2000データ削減
HKL-2000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: 2.4→29.319 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7142 / SU ML: 0.33 / σ(F): 0 / 位相誤差: 33.35 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2514 3233 5.06 %RANDOM
Rwork0.2158 ---
all0.2176 66802 --
obs0.2176 63877 89.92 %-
溶媒の処理減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 26.313 Å2 / ksol: 0.324 e/Å3
原子変位パラメータBiso max: 126.59 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--8.145 Å2-0 Å20 Å2
2---8.145 Å20 Å2
3---16.29 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→29.319 Å
タンパク質核酸リガンド溶媒全体
原子数10322 0 0 541 10863
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0210616
X-RAY DIFFRACTIONf_angle_d1.79214440
X-RAY DIFFRACTIONf_dihedral_angle_d14.2673658
X-RAY DIFFRACTIONf_chiral_restr0.1131586
X-RAY DIFFRACTIONf_plane_restr0.0081830
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1706X-RAY DIFFRACTIONPOSITIONAL0.065
12B1706X-RAY DIFFRACTIONPOSITIONAL0.065
13C1706X-RAY DIFFRACTIONPOSITIONAL0.086
14D1712X-RAY DIFFRACTIONPOSITIONAL0.091
15E1706X-RAY DIFFRACTIONPOSITIONAL0.142
16F1706X-RAY DIFFRACTIONPOSITIONAL0.096
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4005-2.48620.39052680.3035516677
2.4862-2.58570.30362870.2758541281
2.5857-2.70330.31712960.2757563084
2.7033-2.84570.31833160.2479577287
2.8457-3.02390.26893400.2299599189
3.0239-3.2570.25083210.2294617592
3.257-3.58430.25943220.2295646595
3.5843-4.10180.23293720.1921656198
4.1018-5.16320.18113630.158664198
5.1632-29.32070.22583480.1954683197
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)
10.12540.0381-0.17240.2861-0.18390.3037-0.1485-0.00180.12310.0014-0.0163-0.034-0.0092-0.0216-0.19360.2541-0.1938-0.090.2629-0.0790.211367.871487.5689154.9489
20.0429-0.05790.06970.0813-0.09430.16170.06510.02830.0473-0.0433-0.0269-0.151-0.03160.19170.00010.2658-0.0945-0.0720.2991-0.06040.521582.098895.9587147.3281
30.022-0.0113-0.00730.00630.00470.008-0.0541-0.0846-0.00180.0475-0.01890.01680.01450.0412-0.00090.4413-0.119-0.19880.27860.08940.440169.381580.1653156.2984
40.0029-0.0031-0.01580.02230.06840.19870.08510.06360.0561-0.00870.0888-0.07330.03860.0490.08490.0366-0.0227-0.07150.16260.0270.371669.456884.6617144.6881
50.0239-0.0162-0.00450.0234-0.02120.0488-0.0721-0.01190.057-0.0252-0.0547-0.0156-0.03850.01-0.08010.2601-0.1244-0.01650.201-0.00470.646465.865897.7444138.4807
60.0111-0.01460.01650.0198-0.02010.0260.0166-0.0125-0.04620.02210.0185-0.02950.02170.02250.03140.1127-0.0162-0.08260.187-0.10710.303672.063482.3102139.6374
70.02370.01580.01860.01470.00160.04010.0360.033-0.0148-0.0380.01460.0167-0.0065-0.02820.00830.33830.0072-0.08970.44950.0010.186372.960583.0339134.2615
80.0728-0.0458-0.04760.03090.03490.04340.03170.1079-0.0974-0.01990.168-0.1118-0.01560.16040.11360.1877-0.1498-0.11880.30610.03550.521977.828884.8479142.0829
90.0543-0.0152-0.0030.02230.02850.0490.0789-0.0154-0.0778-0.0330.0828-0.05270.029-0.03480.48960.1318-0.0166-0.18350.34480.04490.459479.663991.6858142.9657
100.0107-0.0141-0.0020.0320.00650.0016-0.00030.02180.0241-0.0461-0.02930.0154-0.0380.0325-0.16960.0952-0.2803-0.33060.29630.15140.389271.000294.8963144.7466
110.11640.008-0.14430.0067-0.02150.21110.0691-0.08190.03290.00350.03220.0438-0.02390.03730.10340.094-0.086-0.08350.2927-0.14030.287462.884184.181149.2886
120.0079-0.0085-0.00870.01580.0060.058-0.03590.2112-0.0019-0.1514-0.0677-0.08540.0135-0.08060.00070.4524-0.2075-0.02110.5395-0.05060.413272.758798.9912141.3735
130.01280.0150.00650.01820.0010.0685-0.01460.03850.02940.0360.0063-0.0056-0.1017-0.03370.08010.1898-0.0218-0.06520.17790.00470.110253.22494.9078132.9964
140.0576-0.04580.02940.0385-0.03740.11390.052-0.0040.0078-0.00360.03060.0097-0.0346-0.00080.01020.39290.124-0.1450.2012-0.13080.437541.3481104.9533147.2986
150.2602-0.0301-0.08610.00780.00840.1730.0032-0.16620.14030.06880.0046-0.0179-0.1064-0.05110.06150.1457-0.00790.03510.1453-0.07570.093552.352289.2135138.1676
160.34360.0449-0.2360.1076-0.05810.3776-0.08630.10930.0195-0.03790.0263-0.00030.0511-0.1304-0.09730.01990.0083-0.15580.02460.01980.08951.335985.0819146.2561
170.0027-0.00980.01370.0376-0.04620.05820.0019-0.00290.0324-0.07370.03310.01310.00750.06580.03120.1678-0.1237-0.01130.1617-0.15050.11545.321890.298151.7089
180.0099-0.0483-0.01110.17190.05220.0126-0.03210.07-0.0569-0.00650.03880.01620.0899-0.01170.03130.06710.01250.01970.0003-0.1438-0.003444.222888.7606135.6639
190.0722-0.09290.05810.1038-0.06810.0475-0.0227-0.16260.18520.1144-0.09810.0475-0.0424-0.1469-0.10760.1793-0.03140.00690.1843-0.09360.276650.42196.517146.224
200.35790.0667-0.04390.31460.080.32220.0143-0.0314-0.07210.0837-0.0385-0.0138-0.01110.2752-0.20220.029-0.0782-0.0360.1007-0.01950.229858.382188.1827139.3733
210.00380.0012-0.00030.0032-0.01160.03370.02360.03820.11940.0293-0.0654-0.0899-0.09360.0087-0.04220.349-0.04450.13280.04270.08520.282943.2823108.680198.1598
220.0864-0.0129-0.03580.0194-0.01530.0367-0.0736-0.00920.0351-0.03080.02970.0278-0.0531-0.0559-0.04840.4629-0.0021-0.06770.17390.11730.291337.9295113.686100.1648
230.05750.00060.0880.0224-0.00560.13220.0073-0.0140.02830.01960.0107-0.0122-0.0713-0.12450.03190.2101-0.00430.00230.15890.01530.077437.238100.8989102.4029
240.04840.02430.01460.0161-0.00350.0448-0.080.01470.03380.0254-0.064-0.164-0.01610.1312-0.0990.1209-0.0602-0.0250.12250.13680.232345.7442104.8327111.7563
250.00180.0001-0.00160.00240.00170.0020.00840.03660.0167-0.01540.07330.0230.0143-0.0211-0.00020.30870.04380.06830.2286-0.05190.23233.2088103.8596112.2647
260.33790.213-0.11010.1856-0.03010.66880.1165-0.05450.170.18090.08570.0215-0.1365-0.00630.2010.26470.056-0.05140.0991-0.00330.286435.2145110.3597107.1713
270.04610.0042-0.040.02190.04140.1296-0.0006-0.03520.00950.02930.0139-0.0320.00610.0416-0.01130.3694-0.0085-0.00010.1172-0.17710.422445.521118.7104112.3428
280.00140.0051-0.0030.0205-0.00990.0049-0.0052-0.01980.02470.0155-0.0074-0.0308-0.03450.0561-0.03890.21590.074-0.00440.07370.18590.450446.6778108.7883105.4507
290.0268-0.01240.00890.0051-0.00650.0047-0.03660.00370.0061-0.01170.0235-0.026-0.09590.05960.03910.1482-0.0366-0.00350.25710.09660.007639.797493.7992101.5267
300.0184-0.0175-0.00410.0299-0.02850.071-0.05030.01-0.01180.0115-0.0665-0.0967-0.03730.0922-0.07850.29560.01330.14530.07140.2220.245748.9472110.7974100.9346
310.27020.1330.17140.06320.08180.1043-0.05430.14480.0513-0.09310.02990.003-0.1320.0981-0.04550.33360.0677-0.08080.12350.01970.268948.6609100.3228119.4983
320.01540.01550.01130.0378-0.01030.027-0.02210.0393-0.0050.010.0091-0.031-0.02110.04440.01660.1588-0.18460.09420.28710.0860.306363.136192.3728112.0386
330.0051-0.0070.00150.00990.00130.0043-0.05470.0184-0.0398-0.01240.0568-0.0022-0.01060.10130.00040.18740.01660.11090.20060.03920.352366.194986.099105.7676
340.0966-0.02810.04280.09470.02640.0297-0.02990.08890.1062-0.18440.052-0.04160.03320.04420.20050.11430.0202-0.0527-0.44440.4452-0.147649.469490.4486112.3271
350.0971-0.03870.01660.0168-0.00240.00230.01150.0147-0.01190.0572-0.104-0.0340.08120.0204-0.20280.01520.2266-0.0642-0.32750.205-0.030748.857986.8254102.7717
360.02320.00840.00320.00540.0020.0204-0.0362-0.01940.00940.06830.01590.0031-0.0456-0.02610.00390.10290.05590.00420.17030.07710.08655.767682.4116102.4425
370.02610.00150.0381-0.0006-0.00140.0553-0.0255-0.01690.0307-0.00320.0068-0.0307-0.0844-0.0645-0.05450.1827-0.0529-0.13320.09540.09920.004255.109282.7046115.4148
380.00640.0009-0.01690.0160.04430.1472-0.00550.0370.002-0.0825-0.0188-0.09050.03710.0631-0.15580.2494-0.01860.02060.15450.09250.115158.362991.7753104.0117
390.02820.0295-0.08710.2550.03260.3331-0.04490.1260.0059-0.0954-0.0821-0.015-0.09510.005-0.27160.05550.01-0.07420.14330.10430.056740.68794.3224112.6245
400.00840.0028-0.00840.0009-0.00050.0099-0.06060.0468-0.0048-0.0459-0.0404-0.07260.00840.0287-00.2316-0.15170.05630.27910.00320.267563.7895.2424107.0512
410.0121-0.00890.02440.0043-0.01450.0514-0.0426-0.00590.01310.0055-0.0123-0.0007-0.0807-0.017-0.04930.29440.0564-0.0780.0879-0.13950.159153.155749.0925155.4544
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:20)
2X-RAY DIFFRACTION2(chain A and resid 21:33)
3X-RAY DIFFRACTION3(chain A and resid 34:39)
4X-RAY DIFFRACTION4(chain A and resid 40:49)
5X-RAY DIFFRACTION5(chain A and resid 50:56)
6X-RAY DIFFRACTION6(chain A and resid 57:63)
7X-RAY DIFFRACTION7(chain A and resid 64:68)
8X-RAY DIFFRACTION8(chain A and resid 69:80)
9X-RAY DIFFRACTION9(chain A and resid 81:93)
10X-RAY DIFFRACTION10(chain A and resid 94:99)
11X-RAY DIFFRACTION11(chain A and resid 100:113)
12X-RAY DIFFRACTION12(chain A and resid 114:135)
13X-RAY DIFFRACTION13(chain A and resid 136:144)
14X-RAY DIFFRACTION14(chain A and resid 145:151)
15X-RAY DIFFRACTION15(chain A and resid 152:176)
16X-RAY DIFFRACTION16(chain A and resid 177:194)
17X-RAY DIFFRACTION17(chain A and resid 195:203)
18X-RAY DIFFRACTION18(chain A and resid 204:217)
19X-RAY DIFFRACTION19(chain A and resid 218:232)
20X-RAY DIFFRACTION20(chain A and resid 233:253)
21X-RAY DIFFRACTION21(chain B and resid 11:27)
22X-RAY DIFFRACTION22(chain B and resid 28:35)
23X-RAY DIFFRACTION23(chain B and resid 36:49)
24X-RAY DIFFRACTION24(chain B and resid 50:60)
25X-RAY DIFFRACTION25(chain B and resid 61:66)
26X-RAY DIFFRACTION26(chain B and resid 67:88)
27X-RAY DIFFRACTION27(chain B and resid 89:93)
28X-RAY DIFFRACTION28(chain B and resid 94:99)
29X-RAY DIFFRACTION29(chain B and resid 100:109)
30X-RAY DIFFRACTION30(chain B and resid 110:116)
31X-RAY DIFFRACTION31(chain B and resid 117:138)
32X-RAY DIFFRACTION32(chain B and resid 139:146)
33X-RAY DIFFRACTION33(chain B and resid 147:154)
34X-RAY DIFFRACTION34(chain B and resid 155:176)
35X-RAY DIFFRACTION35(chain B and resid 177:198)
36X-RAY DIFFRACTION36(chain B and resid 199:205)
37X-RAY DIFFRACTION37(chain B and resid 206:217)
38X-RAY DIFFRACTION38(chain B and resid 218:232)
39X-RAY DIFFRACTION39(chain B and resid 233:246)
40X-RAY DIFFRACTION40(chain B and resid 247:252)
41X-RAY DIFFRACTION41(chain C and resid 11:20)
42X-RAY DIFFRACTION42(chain C and resid 21:33)
43X-RAY DIFFRACTION43(chain C and resid 34:39)
44X-RAY DIFFRACTION44(chain C and resid 40:49)
45X-RAY DIFFRACTION45(chain C and resid 50:56)
46X-RAY DIFFRACTION46(chain C and resid 57:63)
47X-RAY DIFFRACTION47(chain C and resid 64:68)
48X-RAY DIFFRACTION48(chain C and resid 69:88)
49X-RAY DIFFRACTION49(chain C and resid 89:93)
50X-RAY DIFFRACTION50(chain C and resid 94:99)
51X-RAY DIFFRACTION51(chain C and resid 100:109)
52X-RAY DIFFRACTION52(chain C and resid 110:117)
53X-RAY DIFFRACTION53(chain C and resid 135:146)
54X-RAY DIFFRACTION54(chain C and resid 147:156)
55X-RAY DIFFRACTION55(chain C and resid 157:176)
56X-RAY DIFFRACTION56(chain C and resid 177:194)
57X-RAY DIFFRACTION57(chain C and resid 195:201)
58X-RAY DIFFRACTION58(chain C and resid 202:217)
59X-RAY DIFFRACTION59(chain C and resid 218:232)
60X-RAY DIFFRACTION60(chain C and resid 233:252)
61X-RAY DIFFRACTION61(chain D and resid 11:20)
62X-RAY DIFFRACTION62(chain D and resid 21:33)
63X-RAY DIFFRACTION63(chain D and resid 34:39)
64X-RAY DIFFRACTION64(chain D and resid 40:49)
65X-RAY DIFFRACTION65(chain D and resid 50:59)
66X-RAY DIFFRACTION66(chain D and resid 60:65)
67X-RAY DIFFRACTION67(chain D and resid 66:86)
68X-RAY DIFFRACTION68(chain D and resid 87:93)
69X-RAY DIFFRACTION69(chain D and resid 94:99)
70X-RAY DIFFRACTION70(chain D and resid 100:109)
71X-RAY DIFFRACTION71(chain D and resid 110:116)
72X-RAY DIFFRACTION72(chain D and resid 117:137)
73X-RAY DIFFRACTION73(chain D and resid 138:146)
74X-RAY DIFFRACTION74(chain D and resid 147:156)
75X-RAY DIFFRACTION75(chain D and resid 157:176)
76X-RAY DIFFRACTION76(chain D and resid 177:194)
77X-RAY DIFFRACTION77(chain D and resid 195:205)
78X-RAY DIFFRACTION78(chain D and resid 206:217)
79X-RAY DIFFRACTION79(chain D and resid 218:232)
80X-RAY DIFFRACTION80(chain D and resid 233:253)
81X-RAY DIFFRACTION81(chain E and resid 11:21)
82X-RAY DIFFRACTION82(chain E and resid 22:32)
83X-RAY DIFFRACTION83(chain E and resid 33:39)
84X-RAY DIFFRACTION84(chain E and resid 40:49)
85X-RAY DIFFRACTION85(chain E and resid 50:60)
86X-RAY DIFFRACTION86(chain E and resid 61:66)
87X-RAY DIFFRACTION87(chain E and resid 67:80)
88X-RAY DIFFRACTION88(chain E and resid 81:93)
89X-RAY DIFFRACTION89(chain E and resid 94:99)
90X-RAY DIFFRACTION90(chain E and resid 100:109)
91X-RAY DIFFRACTION91(chain E and resid 110:116)
92X-RAY DIFFRACTION92(chain E and resid 117:138)
93X-RAY DIFFRACTION93(chain E and resid 139:146)
94X-RAY DIFFRACTION94(chain E and resid 147:156)
95X-RAY DIFFRACTION95(chain E and resid 157:176)
96X-RAY DIFFRACTION96(chain E and resid 177:191)
97X-RAY DIFFRACTION97(chain E and resid 192:201)
98X-RAY DIFFRACTION98(chain E and resid 202:217)
99X-RAY DIFFRACTION99(chain E and resid 218:232)
100X-RAY DIFFRACTION100(chain E and resid 233:252)
101X-RAY DIFFRACTION101(chain F and resid 11:21)
102X-RAY DIFFRACTION102(chain F and resid 22:34)
103X-RAY DIFFRACTION103(chain F and resid 35:46)
104X-RAY DIFFRACTION104(chain F and resid 47:56)
105X-RAY DIFFRACTION105(chain F and resid 57:63)
106X-RAY DIFFRACTION106(chain F and resid 64:68)
107X-RAY DIFFRACTION107(chain F and resid 69:80)
108X-RAY DIFFRACTION108(chain F and resid 81:93)
109X-RAY DIFFRACTION109(chain F and resid 94:99)
110X-RAY DIFFRACTION110(chain F and resid 100:106)
111X-RAY DIFFRACTION111(chain F and resid 107:113)
112X-RAY DIFFRACTION112(chain F and resid 114:137)
113X-RAY DIFFRACTION113(chain F and resid 138:146)
114X-RAY DIFFRACTION114(chain F and resid 147:156)
115X-RAY DIFFRACTION115(chain F and resid 157:176)
116X-RAY DIFFRACTION116(chain F and resid 177:191)
117X-RAY DIFFRACTION117(chain F and resid 192:201)
118X-RAY DIFFRACTION118(chain F and resid 202:217)
119X-RAY DIFFRACTION119(chain F and resid 218:234)
120X-RAY DIFFRACTION120(chain F and resid 235:252)

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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