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- PDB-5wux: TNFalpha-certolizumab Fab -

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基本情報

登録情報
データベース: PDB / ID: 5wux
タイトルTNFalpha-certolizumab Fab
要素
  • Tumor necrosis factor alpha
  • heavy
  • light
キーワードIMMUNE SYSTEM / antibody
機能・相同性
機能・相同性情報


regulation of multicellular organismal process / regulation of biological quality / regulation of secretion / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation ...regulation of multicellular organismal process / regulation of biological quality / regulation of secretion / negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / positive regulation of interleukin-18 production / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / epithelial cell proliferation involved in salivary gland morphogenesis / positive regulation of hair follicle development / : / death receptor agonist activity / negative regulation of myelination / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of action potential / sequestering of triglyceride / positive regulation of I-kappaB phosphorylation / TNF signaling / positive regulation of protein transport / toll-like receptor 3 signaling pathway / embryonic digestive tract development / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / regulation of immunoglobulin production / positive regulation of calcineurin-NFAT signaling cascade / response to fructose / positive regulation of neuroinflammatory response / cellular response to toxic substance / positive regulation of mononuclear cell migration / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / positive regulation of fever generation / negative regulation of myoblast differentiation / negative regulation of D-glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of cytokine production involved in inflammatory response / regulation of metabolic process / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / positive regulation of podosome assembly / positive regulation of hepatocyte proliferation / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of fat cell differentiation / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / response to L-glutamate / cortical actin cytoskeleton organization / regulation of developmental process / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / regulation of synapse organization / negative regulation of fat cell differentiation / : / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / humoral immune response / negative regulation of apoptotic signaling pathway / skeletal muscle contraction / phagocytic cup
類似検索 - 分子機能
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily ...Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Tumor necrosis factor / Tumor necrosis factor
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: 2.9 Å
データ登録者Heo, Y.S. / Lee, J.U.
引用ジャーナル: Int J Mol Sci / 年: 2017
タイトル: Molecular Basis for the Neutralization of Tumor Necrosis Factor alpha by Certolizumab Pegol in the Treatment of Inflammatory Autoimmune Diseases
著者: Lee, J.U. / Shin, W. / Son, J.Y. / Yoo, K.Y. / Heo, Y.S.
履歴
登録2016年12月21日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02017年6月7日Provider: repository / タイプ: Initial release
改定 1.12024年10月23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: heavy
B: light
C: heavy
D: light
H: heavy
L: light
E: Tumor necrosis factor alpha
F: Tumor necrosis factor alpha
G: Tumor necrosis factor alpha


分子量 (理論値)分子数
合計 (水以外)194,0989
ポリマ－194,0989
非ポリマー00
水00
1
A: heavy
B: light
F: Tumor necrosis factor alpha


分子量 (理論値)分子数
合計 (水以外)64,6993
ポリマ－64,6993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: heavy
D: light
G: Tumor necrosis factor alpha


分子量 (理論値)分子数
合計 (水以外)64,6993
ポリマ－64,6993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
H: heavy
L: light
E: Tumor necrosis factor alpha


分子量 (理論値)分子数
合計 (水以外)64,6993
ポリマ－64,6993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)148.592, 207.219, 112.631
Angle α, β, γ (deg.)90.00, 118.81, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: 抗体 heavy


分子量: 23905.816 Da / 分子数: 3 / 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-Pichia pastoris shuttle vector pPpB1GAP_S (その他)
#2: 抗体 light


分子量: 23423.004 Da / 分子数: 3 / 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-Pichia pastoris shuttle vector pPpARG4 (その他)
#3: タンパク質 Tumor necrosis factor alpha


分子量: 17370.658 Da / 分子数: 3 / Fragment: UNP residues 76-232 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TNF
発現宿主: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (その他)
参照: UniProt: C1K3N5, UniProt: P01375*PLUS
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: 3.91 Å3/Da / 溶媒含有率: 68.57 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1M 3-(cyclohexylamino)-1-propanesulfonic acid pH10.2, 0.2M lithium sulfate, 1.5M ammonium sulfate

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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: PAL/PLS / ビームライン: 7A (6B, 6C1) / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2015年12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: 1 Å / 相対比: 1
反射解像度: 2.9→30 Å / Num. obs: 63355 / % possible obs: 95.2 % / 冗長度: 2.9 % / Net I/σ(I): 19.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.9→30 Å / SU ML: 0.46 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 30.66
Rfactor反射数%反射
Rfree0.2663 3216 5.08 %
Rwork0.2261 --
obs0.2281 63355 95.1 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.9→30 Å
タンパク質核酸リガンド溶媒全体
原子数12793 0 0 0 12793
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00613107
X-RAY DIFFRACTIONf_angle_d1.27817816
X-RAY DIFFRACTIONf_dihedral_angle_d18.3654677
X-RAY DIFFRACTIONf_chiral_restr0.0472001
X-RAY DIFFRACTIONf_plane_restr0.0062276
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8888-2.93190.4461270.37492459X-RAY DIFFRACTION92
2.9319-2.97770.3631270.32232700X-RAY DIFFRACTION97
2.9777-3.02650.33531450.27932664X-RAY DIFFRACTION97
3.0265-3.07860.33761220.27172651X-RAY DIFFRACTION97
3.0786-3.13450.29281280.25672698X-RAY DIFFRACTION97
3.1345-3.19480.30731500.24462641X-RAY DIFFRACTION97
3.1948-3.25990.32861400.26932652X-RAY DIFFRACTION97
3.2599-3.33070.32821500.27812601X-RAY DIFFRACTION95
3.3307-3.40810.36711470.33062512X-RAY DIFFRACTION92
3.4081-3.49320.36391450.35682442X-RAY DIFFRACTION90
3.4932-3.58750.33971650.27382595X-RAY DIFFRACTION95
3.5875-3.69290.37921370.2972627X-RAY DIFFRACTION95
3.6929-3.81190.36431390.27562542X-RAY DIFFRACTION93
3.8119-3.94790.32651280.31492444X-RAY DIFFRACTION89
3.9479-4.10560.28051300.2212579X-RAY DIFFRACTION92
4.1056-4.2920.23361480.19862533X-RAY DIFFRACTION94
4.292-4.51770.21111390.17112641X-RAY DIFFRACTION95
4.5177-4.79980.20991470.16542582X-RAY DIFFRACTION94
4.7998-5.16880.17891390.16292670X-RAY DIFFRACTION97
5.1688-5.68610.22411430.17692707X-RAY DIFFRACTION98
5.6861-6.50230.23391320.20652755X-RAY DIFFRACTION99
6.5023-8.16750.2561600.20482732X-RAY DIFFRACTION99
8.1675-31.0540.19461280.19282712X-RAY DIFFRACTION96
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)
10.1849-0.05430.36140.147-0.12830.16480.11620.03440.22090.2507-0.3158-0.148-0.52510.219300.51-0.1919-0.16390.9314-0.01920.932-17.681927.90671.3629
20.10670.0921-0.21020.6581-0.37990.0656-0.16760.1414-0.02450.2965-0.0314-0.1837-0.53720.379900.1963-0.2059-0.14921.249-0.09180.6406-12.554420.15732.8916
3-0.01390.101-0.1022-0.0219-0.0543-0.0069-0.10380.0642-0.00610.2856-0.12810.0373-0.24220.701900.3871-0.2275-0.0561.16670.05030.6643-10.9421.3974-6.6498
4-0.09850.3883-0.236-0.2588-0.26220.03490.7219-0.19540.058-0.6697-0.6141-0.1158-1.5610.5227-0-0.7316-0.4508-0.28630.9576-0.08090.5768-21.02129.905-16.328
50.06220.2083-0.18760.4398-0.28820.0677-0.3264-0.089-0.05060.23570.0617-0.1261-0.2117-0.049-00.5036-0.18270.08670.4024-0.05590.5103-29.433833.6378-27.265
60.21310.1963-0.29330.1485-0.09270.12-0.0372-0.18860.61650.2506-0.4733-0.1054-0.70960.3205-00.7972-0.2171-0.02950.6145-0.17670.7479-24.237442.0554-23.7092
70.0420.0002-0.06140.0849-0.10440.02740.1160.2212-0.2904-0.0477-0.0419-0.03340.16460.34400.4629-0.0168-0.05710.75440.04180.628-29.1753.8443-13.3211
80.1210.5820.46850.69970.23540.6435-0.0314-0.0531-0.105400.0615-0.06510.0170.2162-00.32480.0071-0.04780.4864-0.02410.4411-29.66727.9707-4.6985
9-0.03380.02970.04420.03910.060.0386-0.2481-0.22010.0794-0.48950.636-0.0337-0.14670.3523-00.401-0.2040.00540.62780.0090.4209-37.101312.9238-26.5529
100.3208-0.14950.42210.0152-0.2020.1331-0.2150.05160.1755-0.22220.16270.14330.0382-0.0195-00.4922-0.1450.05180.366-0.05250.487-25.674833.3643-36.9309
110.03610.0482-0.01690.00790.09730.0026-0.10210.1513-0.3995-0.12580.0398-0.51210.2058-0.144-00.542-0.10610.06340.499-0.060.5965-23.486620.8559-40.718
120.0339-0.03190.03620.03440.00450.03090.3317-0.0770.2794-0.00970.3849-0.4741-0.2056-0.1846-00.5778-0.15290.0050.6586-0.07510.7276-33.551920.3153-24.4823
130.3239-0.371-0.1230.53140.06710.20650.05040.03730.1294-0.2736-0.06120.0019-0.1119-0.053100.6163-0.18340.09610.4896-0.00150.5432-25.472127.9311-43.4444
140.65710.95130.1031-0.3419-0.0341.1638-0.1026-0.30110.17890.08170.1114-0.0586-0.1211-0.1508-00.57530.1458-0.01450.3593-0.09770.3951-81.957113.239736.3193
15-0.023-0.02010.05530.0204-0.0023-0.00490.9372-0.2893-0.99720.41270.34920.1415-0.84950.362800.440.48140.47470.96030.36311.0263-102.312-8.61238.029
160.6428-0.6871-0.29190.27960.49290.5485-0.05210.2144-0.1462-0.22510.00120.0314-0.16770.051900.50610.0693-0.02750.3216-0.05730.3244-77.41630.493817.7615
170.2101-0.00880.28350.09260.24390.04220.08890.22390.03280.19130.15190.143-0.0321-0.0671-00.6370.06080.20510.7120.14910.7336-109.3274-11.433528.6048
180.05870.1872-0.1630.4177-0.18860.3836-0.16250.2789-0.15630.08710.36750.0747-0.0238-0.013800.5505-0.02460.01010.52870.02930.7788-109.519-8.355623.3811
190.19010.01780.24810.0609-0.13170.1676-0.10470.3205-0.0146-0.03090.20750.65080.0386-0.1474-00.757-0.09010.11890.77330.03421.3417-117.0646-15.823422.6518
20-0.05030.01990.02090.12640.2710.1398-0.13380.2461-0.19120.2572-0.0506-0.17310.16880.596800.63520.18670.04960.79170.13480.6053-23.3864-44.254236.6718
210.1857-0.4160.62720.6138-0.33570.1968-0.071-0.07440.02620.18150.01640.1507-0.02520.090400.61480.16690.05360.82320.01190.4531-31.1712-35.722839.7434
22-0.0006-0.1131-0.29680.22310.23860.30870.0638-0.0816-0.16010.0627-0.11750.13590.03310.15400.52260.1820.0390.7640.00550.4529-30.7589-38.870536.0293
23-0.2533-0.1479-0.11440.3163-0.07390.04240.1649-0.5024-0.6002-0.2283-0.3861-0.2644-0.72360.5356-00.53060.17740.18850.75310.22210.7897-17.395-59.57825.192
24-0.03960.02360.02-0.03150.00480.03910.13960.3837-0.10210.1811-0.1078-0.1182-0.36860.2732-00.87960.05630.16640.82160.01290.8148-15.1597-52.305323.3469
250.1349-0.18470.05120.11410.12060.11980.1357-0.0571-0.6049-0.1627-0.1211-0.45560.09040.5282-00.78110.16410.2060.93450.04090.9305-20.3143-55.981218.2437
26-0.0630.0472-0.11140.01260.0004-0.06670.4280.09340.0601-1.01480.2959-0.05050.0525-0.2987-00.70720.39941.15391.00260.46860.9561-10.602-54.78319.519
270.39070.2760.1570.43540.11910.0331-0.1031-0.0671-0.1137-0.3029-0.08130.2931-0.2626-0.1297-00.58960.2852-0.00480.5492-0.07630.4534-44.0744-35.850618.7688
280.13750.13010.330.37160.59480.21960.1469-0.0502-0.0509-0.11930.04240.07910.02490.0257-00.50520.19650.02640.5803-0.02670.4037-36.9625-29.541618.2429
29-0.2493-0.3051-0.1460.3517-0.17680.0004-0.0402-0.2034-0.2844-0.13450.0260.2158-0.26330.104600.60.18440.07240.6672-0.02820.4966-38.812-36.045621.3413
300.02640.09710.11360.24980.3782-0.12980.4093-0.075-0.7496-0.8649-0.00450.56140.19810.494501.10380.56780.23941.0257-0.18880.6681-20.5295-59.50739.5592
310.0695-0.02670.0742-0.00490.07440.0483-0.50010.25420.1687-0.32790.1692-0.4380.5875-0.117901.05190.24170.12740.5873-0.05160.5043-26.516-62.5497.749
32-0.2272-0.08060.07320.0051-0.1123-0.06320.2378-0.23680.0965-0.44270.0842-0.18490.16980.210201.09160.24860.13140.9573-0.11130.7824-23.0499-62.000911.9787
330.0266-0.0417-0.0595-0.0247-0.05310.0271-0.1151-0.353-0.1596-0.54710.98740.60650.71390.4954-01.43580.4592-0.0930.9071-0.28771.1019-24.4746-67.59780.4995
34-0.09420.14510.06-0.0309-0.0206-0.0438-0.3656-0.57980.6869-0.258-0.25870.6075-0.11730.20400.65260.1852-0.19670.895-0.26510.5773-43.062116.666619.5667
35-0.0093-0.00620.0086-0.00210.00420.0351-0.0329-0.039-0.1492-0.00030.0045-0.06010.14-0.0076-00.4921-0.9021-2.61980.6015-0.9963-2.4579-41.44218.67826.062
360.2883-0.2932-0.15980.21670.1070.0588-0.15140.1085-0.0847-0.05340.3859-0.1159-0.26510.4366-00.5771-0.0202-0.0970.7674-0.06510.356-36.431712.586621.1183
370.00880.0211-0.0114-0.0357-0.05360.0096-0.38470.386-0.3465-1.2115-0.2467-0.45140.14460.2422-00.80910.0987-0.02590.8841-0.0130.4912-46.6776-0.7939-1.1372
38-0.04050.02310.0268-0.0573-0.0043-0.0394-0.11780.04030.03140.05030.1080.05120.02030.4466-00.39330.0028-0.05940.7141-0.06630.4506-29.73827.187915.139
390.04070.01360.0290.02650.03190.0547-0.06320.0565-0.0919-0.09120.104-0.06380.1353-0.011900.95540.0389-0.18380.64270.01470.6013-52.781-2.8233.192
400.0197-0.0452-0.14890.0869-0.01820.15950.32390.44450.11530.0527-0.067-0.12370.1120.01600.4643-0.0513-0.02080.6638-0.03430.4868-40.542.812418.4048
410.00270.03-0.0353-0.17310.1826-0.038-0.05880.610.12330.142-0.3446-0.0987-0.13720.1665-00.4265-0.0198-0.17640.8261-0.10910.7504-29.923413.566519.4716
42-00.1642-0.16140.04030.01630.046-0.3374-0.17040.5794-0.1462-0.15420.0332-0.6676-0.289700.35370.0878-0.07320.7463-0.17730.4486-45.04829.475515.554
430.247-0.1259-0.26150.0062-0.03330.1094-0.1754-0.37520.04920.39660.40020.06440.2577-0.387900.52970.15580.02770.5655-0.05520.4019-53.2613-6.699936.4532
44-0.0154-0.09570.0998-0.02380.0083-0.0058-0.0849-0.6793-0.49110.301-0.03850.5248-0.28850.605700.81360.1790.00320.88950.03940.4138-50.6593-8.365339.9722
450.0529-0.11310.1265-0.0096-0.00290.0022-0.5166-0.01340.39890.78420.53790.80750.22240.312100.59950.10670.0220.562-0.17630.4438-54.66674.06241.3174
460.1168-0.0614-0.05-0.04590.0719-0.0350.0004-0.42530.1234-0.0125-0.09510.18440.02470.2751-00.5095-0.0446-0.04740.609-0.07010.5484-49.2231-1.491127.8952
470.030.01750.03280.0070.07330.0072-0.10070.2355-0.45060.04180.4748-0.20590.7435-0.639600.7713-0.0989-0.03430.5578-0.07960.7994-61.8305-9.811510.0759
48-0.0193-0.1853-0.1208-0.13210.0220.001-0.03650.01560.02750.13250.2110.06270.00140.6221-00.52580.01940.02380.2132-0.0220.4719-57.20897.57127.139
490.00040.00590.01190.00250.00690.0361-0.11110.1022-0.3422-0.16120.142-0.0147-0.1055-0.1445-00.95570.20220.080.79190.43280.5811-55.485-12.5848.607
500.0737-0.0066-0.1855-0.02350.0632-0.0223-0.0509-0.2068-0.17320.07770.07830.2074-0.07670.199100.44510.09960.04220.4921-0.03250.4566-48.9716-0.449723.694
510.0089-0.07750.03620.0132-0.0110.017-0.4481-0.6343-0.37630.17940.28710.2649-0.03110.118200.64520.1192-0.050.4239-0.04720.3526-56.35496.739234.7634
520.0739-0.24320.00090.2382-0.16410.22430.2263-0.25980.0060.1605-0.23150.07570.1475-0.211700.38840.05170.05580.5187-0.07080.3941-52.9404-7.226627.5814
530.10830.0992-0.17690.0417-0.032-0.0338-0.1150.309-0.05270.1244-0.3030.4732-0.25210.470900.3875-0.05120.01690.665-0.09840.4185-25.7249-6.076924.8113
54-0.0352-0.1086-0.03510.1933-0.0625-0.00640.58240.0091-0.4460.334-0.599-0.4942-0.2312-0.3337-00.55190.1053-0.1221.10440.01170.5373-23.3989-4.796726.2916
550.29290.05820.12020.17220.0059-0.02620.0015-0.16380.04260.11720.018-0.12740.23790.51900.51760.2366-0.01160.7515-0.03420.3566-31.8591-8.540729.5201
560.0169-0.05730.01330.03880.00170.01670.6009-0.096-0.2716-0.29890.0415-0.22170.8284-0.0988-01.3183-0.06380.01740.8498-0.32311.022-43.4645-19.23295.5843
57-0.00310.022-0.044-0.2064-0.0871-0.0368-0.3007-0.22750.47630.0961-0.02990.10110.1510.135300.61380.25790.00670.6944-0.00220.4023-40.0707-15.830129.6067
580.022-0.00610.01760.0007-0.00240.01640.1117-0.0135-0.0126-0.18180.01160.01890.02290.0467-00.1840.2285-0.27932.0948-0.30390.6986-44.255-12.3092.96
590.0828-0.07820.0388-0.06990.00930.0117-0.005-0.0912-0.0904-0.03680.15950.12520.04410.216900.37450.1381-0.02810.4615-0.04610.3556-40.4725-6.788123.1369
600.08240.1684-0.07740.147-0.3021-0.0332-0.1667-0.0941-0.09540.1250.0972-0.02770.17220.654500.54220.1877-0.05460.8033-0.0620.377-32.8525-9.843823.9283
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 83 )
3X-RAY DIFFRACTION3chain 'H' and (resid 84 through 98 )
4X-RAY DIFFRACTION4chain 'H' and (resid 99 through 162 )
5X-RAY DIFFRACTION5chain 'H' and (resid 163 through 199 )
6X-RAY DIFFRACTION6chain 'H' and (resid 200 through 220 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 18 )
8X-RAY DIFFRACTION8chain 'L' and (resid 19 through 102 )
9X-RAY DIFFRACTION9chain 'L' and (resid 103 through 113 )
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 139 )
11X-RAY DIFFRACTION11chain 'L' and (resid 140 through 160 )
12X-RAY DIFFRACTION12chain 'L' and (resid 161 through 172 )
13X-RAY DIFFRACTION13chain 'L' and (resid 173 through 213 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 124 )
15X-RAY DIFFRACTION15chain 'A' and (resid 125 through 218 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 113 )
17X-RAY DIFFRACTION17chain 'B' and (resid 114 through 144 )
18X-RAY DIFFRACTION18chain 'B' and (resid 145 through 185 )
19X-RAY DIFFRACTION19chain 'B' and (resid 186 through 212 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 17 )
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 76 )
22X-RAY DIFFRACTION22chain 'C' and (resid 77 through 111 )
23X-RAY DIFFRACTION23chain 'C' and (resid 112 through 150 )
24X-RAY DIFFRACTION24chain 'C' and (resid 151 through 162 )
25X-RAY DIFFRACTION25chain 'C' and (resid 163 through 180 )
26X-RAY DIFFRACTION26chain 'C' and (resid 181 through 216 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 38 )
28X-RAY DIFFRACTION28chain 'D' and (resid 39 through 75 )
29X-RAY DIFFRACTION29chain 'D' and (resid 76 through 102 )
30X-RAY DIFFRACTION30chain 'D' and (resid 103 through 129 )
31X-RAY DIFFRACTION31chain 'D' and (resid 130 through 158 )
32X-RAY DIFFRACTION32chain 'D' and (resid 159 through 188 )
33X-RAY DIFFRACTION33chain 'D' and (resid 189 through 208 )
34X-RAY DIFFRACTION34chain 'E' and (resid 9 through 27 )
35X-RAY DIFFRACTION35chain 'E' and (resid 28 through 41 )
36X-RAY DIFFRACTION36chain 'E' and (resid 42 through 66 )
37X-RAY DIFFRACTION37chain 'E' and (resid 67 through 75 )
38X-RAY DIFFRACTION38chain 'E' and (resid 76 through 98 )
39X-RAY DIFFRACTION39chain 'E' and (resid 99 through 113 )
40X-RAY DIFFRACTION40chain 'E' and (resid 114 through 126 )
41X-RAY DIFFRACTION41chain 'E' and (resid 127 through 136 )
42X-RAY DIFFRACTION42chain 'E' and (resid 137 through 157 )
43X-RAY DIFFRACTION43chain 'F' and (resid 9 through 27 )
44X-RAY DIFFRACTION44chain 'F' and (resid 28 through 38 )
45X-RAY DIFFRACTION45chain 'F' and (resid 39 through 53 )
46X-RAY DIFFRACTION46chain 'F' and (resid 54 through 66 )
47X-RAY DIFFRACTION47chain 'F' and (resid 67 through 75 )
48X-RAY DIFFRACTION48chain 'F' and (resid 76 through 98 )
49X-RAY DIFFRACTION49chain 'F' and (resid 99 through 113 )
50X-RAY DIFFRACTION50chain 'F' and (resid 114 through 126 )
51X-RAY DIFFRACTION51chain 'F' and (resid 127 through 136 )
52X-RAY DIFFRACTION52chain 'F' and (resid 137 through 157 )
53X-RAY DIFFRACTION53chain 'G' and (resid 9 through 25 )
54X-RAY DIFFRACTION54chain 'G' and (resid 26 through 41 )
55X-RAY DIFFRACTION55chain 'G' and (resid 42 through 66 )
56X-RAY DIFFRACTION56chain 'G' and (resid 67 through 74 )
57X-RAY DIFFRACTION57chain 'G' and (resid 75 through 99 )
58X-RAY DIFFRACTION58chain 'G' and (resid 100 through 113 )
59X-RAY DIFFRACTION59chain 'G' and (resid 114 through 126 )
60X-RAY DIFFRACTION60chain 'G' and (resid 127 through 157 )

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万見について

-
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