[日本語] English
- PDB-5b8c: High resolution structure of the human PD-1 in complex with pembr... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5b8c
タイトルHigh resolution structure of the human PD-1 in complex with pembrolizumab Fv
要素
  • Pembrolizumab heavy chain variable region (PemVH)
  • Pembrolizumab light chain variable region (PemVL)
  • Programmed cell death protein 1
キーワードIMMUNE SYSTEM / antibody
機能・相同性
機能・相同性情報


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
類似検索 - 分子機能
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Programmed cell death protein 1
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: 2.146 Å
データ登録者Horita, S. / Shimamura, T. / Iwata, S. / Nomura, N.
資金援助 日本, 4件
組織認可番号
Japan Science and Technology Agency (JST) 日本
Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan 日本
Japan Society for the Promotion of Science15K06968 日本
Japan Society for the Promotion of Science15J04343 日本
引用ジャーナル: Sci Rep / : 2016
タイトル: High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1
著者: Horita, S. / Nomura, Y. / Sato, Y. / Shimamura, T. / Iwata, S. / Nomura, N.
履歴
登録2016年6月14日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02016年10月26日Provider: repository / タイプ: Initial release
改定 1.12017年9月27日Group: Data collection / Derived calculations
カテゴリ: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
改定 1.22017年10月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32023年11月8日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
集合体

登録構造単位
A: Pembrolizumab light chain variable region (PemVL)
B: Pembrolizumab heavy chain variable region (PemVH)
C: Programmed cell death protein 1
D: Pembrolizumab light chain variable region (PemVL)
E: Pembrolizumab heavy chain variable region (PemVH)
F: Programmed cell death protein 1
G: Pembrolizumab light chain variable region (PemVL)
H: Pembrolizumab heavy chain variable region (PemVH)
I: Programmed cell death protein 1
J: Pembrolizumab light chain variable region (PemVL)
K: Pembrolizumab heavy chain variable region (PemVH)
L: Programmed cell death protein 1


分子量 (理論値)分子数
合計 (水以外)168,00212
ポリマ-168,00212
非ポリマー00
4,882271
1
A: Pembrolizumab light chain variable region (PemVL)
B: Pembrolizumab heavy chain variable region (PemVH)
C: Programmed cell death protein 1


分子量 (理論値)分子数
合計 (水以外)42,0013
ポリマ-42,0013
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-21 kcal/mol
Surface area14800 Å2
手法PISA
2
D: Pembrolizumab light chain variable region (PemVL)
E: Pembrolizumab heavy chain variable region (PemVH)
F: Programmed cell death protein 1


分子量 (理論値)分子数
合計 (水以外)42,0013
ポリマ-42,0013
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-24 kcal/mol
Surface area14770 Å2
手法PISA
3
G: Pembrolizumab light chain variable region (PemVL)
H: Pembrolizumab heavy chain variable region (PemVH)
I: Programmed cell death protein 1


分子量 (理論値)分子数
合計 (水以外)42,0013
ポリマ-42,0013
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-21 kcal/mol
Surface area14780 Å2
手法PISA
4
J: Pembrolizumab light chain variable region (PemVL)
K: Pembrolizumab heavy chain variable region (PemVH)
L: Programmed cell death protein 1


分子量 (理論値)分子数
合計 (水以外)42,0013
ポリマ-42,0013
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-20 kcal/mol
Surface area14670 Å2
手法PISA
単位格子
Length a, b, c (Å)143.680, 143.130, 76.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

#1: 抗体
Pembrolizumab light chain variable region (PemVL)


分子量: 12991.460 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Brevibacillus choshinensis (バクテリア)
#2: 抗体
Pembrolizumab heavy chain variable region (PemVH)


分子量: 13494.995 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Brevibacillus choshinensis (バクテリア)
#3: タンパク質
Programmed cell death protein 1 / hPD-1


分子量: 15514.168 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PDCD1, PD1 / 発現宿主: Brevibacillus choshinensis (バクテリア) / 参照: UniProt: Q15116
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 271 / 由来タイプ: 天然 / : H2O
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.34 Å3/Da / 溶媒含有率: 47.49 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 20 % PEG 3350, 0.2 M KNO3

-
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: SPring-8 / ビームライン: BL41XU / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年5月11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: 2.146→45.418 Å / Num. obs: 86668 / % possible obs: 99.6 % / 冗長度: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.5
反射 シェル解像度: 2.15→2.2 Å

-
解析

ソフトウェア
名称バージョン分類
PHENIX(dev_2210: ???)精密化
XDSデータ削減
XDS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
開始モデル: 3RRQ, 5DK3
解像度: 2.146→45.418 Å / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 31.18
Rfactor反射数%反射
Rfree0.2259 4460 5.15 %
Rwork0.1839 --
obs0.186 86668 99.65 %
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: 2.146→45.418 Å
タンパク質核酸リガンド溶媒全体
原子数10591 0 0 271 10862
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00410860
X-RAY DIFFRACTIONf_angle_d0.7314763
X-RAY DIFFRACTIONf_dihedral_angle_d16.0496401
X-RAY DIFFRACTIONf_chiral_restr0.0481608
X-RAY DIFFRACTIONf_plane_restr0.0051906
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1464-2.18340.34482200.30734011X-RAY DIFFRACTION93
2.1834-2.22310.31262380.29084001X-RAY DIFFRACTION94
2.2231-2.26590.34182330.28434066X-RAY DIFFRACTION94
2.2659-2.31220.33382130.28454098X-RAY DIFFRACTION95
2.3122-2.36240.31732360.27774019X-RAY DIFFRACTION94
2.3624-2.41740.34972500.27664070X-RAY DIFFRACTION94
2.4174-2.47780.32672260.27734060X-RAY DIFFRACTION95
2.4778-2.54480.33452130.26594094X-RAY DIFFRACTION95
2.5448-2.61970.32622260.24964085X-RAY DIFFRACTION95
2.6197-2.70420.30631890.23424137X-RAY DIFFRACTION96
2.7042-2.80090.22932020.2124098X-RAY DIFFRACTION95
2.8009-2.9130.22831980.20244112X-RAY DIFFRACTION95
2.913-3.04560.24521880.20154141X-RAY DIFFRACTION95
3.0456-3.20610.25272000.18814115X-RAY DIFFRACTION95
3.2061-3.40690.21742360.18274119X-RAY DIFFRACTION94
3.4069-3.66980.19752310.16694138X-RAY DIFFRACTION95
3.6698-4.03890.19042430.14964114X-RAY DIFFRACTION94
4.0389-4.62290.18762300.1264165X-RAY DIFFRACTION95
4.6229-5.82240.15072300.12884209X-RAY DIFFRACTION94
5.8224-45.42830.19262360.16744368X-RAY DIFFRACTION94
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.2951-6.74837.3725.1551-5.94317.222-0.66-0.6868-0.10491.29580.6894-0.2356-1.3345-0.86180.0040.5869-0.040.05450.4718-0.04460.2379-11.478510.118830.4137
24.0363-0.3762-1.49784.7121-0.09320.5832-0.26690.38670.6157-0.06710.23820.286-0.6558-0.0217-0.0160.4717-0.04430.0640.52060.08460.2613-14.651315.46115.6728
31.3286-0.5966-0.79581.5242-0.08811.6173-0.17670.15220.0739-0.00850.1416-0.4279-0.279-0.0059-0.04690.4604-0.04030.0960.5717-0.0068-0.0228-10.9881.99222.2524
43.071-0.56590.85881.4420.26590.93790.21290.26260.4208-0.3072-0.2079-0.15710.23390.0657-0.03130.4891-0.05360.08250.47190.0090.1939-7.16924.400815.6165
55.8145-0.84140.88485.59330.8620.46850.24910.18890.4553-0.4177-0.00120.2116-0.1464-0.2582-0.13770.3951-0.08270.04980.49410.03240.2-17.31397.503415.2275
60.4696-0.03760.2731.818-0.58823.6480.0504-0.0577-0.00610.46510.0207-0.1321-0.39430.38860.02290.4528-0.04920.030.66350.02560.0787-10.79481.745531.7278
72.0065-7.65856.96046.9436-5.87175.104-0.32770.25030.0902-0.17650.52760.7087-0.8007-0.1691-0.2270.5667-0.0441-0.03830.6050.07520.3569-22.929115.443814.35
81.94440.45561.35183.0766-0.79152.32690.10720.3289-0.1549-0.0927-0.09450.464-0.1098-0.8346-0.13270.433-0.02720.01310.52240.0940.1577-30.8175-10.604928.3972
96.913-1.8585-6.55941.47563.21658.4090.28440.59060.1002-0.146-0.133-0.031-0.0195-0.6922-0.03850.4720.04120.0090.53330.05570.157-22.9828-16.516324.6707
100.16420.0570.19710.2066-0.28140.8041-0.16990.147-0.09040.0570.07210.04580.04070.1198-0.0510.419-0.07030.0680.7194-0.0417-0.0387-16.6853-11.069827.3244
110.3079-0.17350.07970.7947-0.26791.49-0.1054-0.49110.44860.52410.31140.3881-0.0891-0.25080.12290.49330.08750.05570.7458-0.0167-0.4107-17.5882-6.548134.8541
122.1044-1.0495-0.41583.91691.03741.660.0486-0.4857-0.06180.6742-0.08-0.17020.0220.16830.05070.56520.00790.04410.68960.03620.1491-21.5259-13.958537.9834
132.5584-1.6481-0.36428.29075.77554.5360.0327-0.3256-0.29980.53580.05540.21730.023-0.3545-0.11570.4142-0.01090.01120.47120.06010.1879-23.7731-18.114130.504
144.10432.2942-0.45725.613-5.17365.7839-0.901-1.0375-0.0751.30870.4842-0.08-0.3925-1.07760.4030.56980.0980.0910.6410.0160.2704-31.3966-2.376140.5925
150.7334-0.17030.24030.4576-0.360.29820.08120.0857-0.02180.0181-0.01020.11340.0811-0.0195-0.06970.4362-0.01290.0550.50670.03810.1434-19.631-7.443425.9111
161.7427-0.7726-1.03721.11950.35321.91170.0610.49250.2977-0.2132-0.0337-0.1798-0.10340.0593-0.05670.3926-0.03120.05010.4841-0.00780.1713-12.9546-8.707522.0708
171.86932.37753.59993.46434.50666.93530.5044-0.4827-0.0348-0.5118-0.55090.8921-0.3011-1.11690.04650.46410.04410.02750.67090.01450.2539-35.7814-3.317833.6052
182.3603-2.0871-0.54082.656-1.59038.55720.0513-0.48570.15470.4993-0.1071-0.36080.01991.0688-0.04220.3542-0.0557-0.12110.5758-0.07130.329811.0011-22.990629.6539
191.9676-2.13373.0796.8274-7.6168.8289-0.1019-0.25820.22450.95360.2216-0.1692-1.1860.1923-0.16120.4357-0.03360.02790.5573-0.07640.238610.7991-13.432124.7985
200.8953-0.1342-0.20885.35160.77440.13680.3115-0.0180.14630.443-0.20930.13390.01590.324-0.08250.38480.0024-0.03640.5116-0.02270.18722.4716-17.517926.3382
212.71232.8408-2.18936.8169-3.7994.9442-0.4243-0.01430.0425-0.36620.82140.25340.2524-0.2009-0.37020.43510.07270.0270.55420.00110.1921-2.6663-21.366727.8867
223.0365-1.3831-1.45110.9043-0.30773.6334-0.0235-0.95150.53780.14420.2264-0.2273-0.03830.0843-0.18110.42120.0119-0.040.5014-0.05910.23815.7475-12.483233.2315
231.598-1.5274-2.41741.46262.30633.6603-0.3104-0.6528-0.04432.0811-0.39820.28531.2489-0.39750.75520.8191-0.066-0.04070.7186-0.02930.33183.1481-25.756142.3027
240.9413-1.6586-0.41659.16090.30640.20110.19370.1856-0.0043-0.436-0.031-0.17990.1264-0.0792-0.26250.3864-0.03040.00890.5656-0.03180.17982.6272-17.819320.0052
254.93052.86991.60474.71680.50291.4719-0.3044-0.6906-0.11491.5888-0.0404-0.37470.2937-0.12330.32690.75770.1888-0.03840.5419-0.00580.37637.9229-31.659437.2191
261.6793-0.70691.94186.58542.6544.14660.380.6125-0.0437-0.5162-0.0640.0735-0.2806-0.5258-0.27380.40830.0007-0.05610.64740.01910.178-46.2035-23.828-11.5592
273.08390.19723.32335.1259-1.67594.24340.0315-0.37010.20630.16510.23530.21050.3701-0.8717-0.19840.3928-0.03060.04670.60030.04020.3835-53.2838-17.53456.9243
285.9996-3.8696-4.94365.53921.51635.32410.0367-0.823-0.6416-0.0006-0.47980.0987-0.53540.62330.41480.3158-0.0578-0.05910.53350.03950.3025-48.9374-25.292-2.3603
295.78651.1463-0.91438.5807-2.25375.51460.03010.6424-0.0491-0.9713-0.49390.02240.5790.19660.3820.3250.0279-0.01920.46850.01360.2363-38.246-34.9232-9.3576
302.3266-0.9507-1.43984.9896-1.06541.51270.0388-0.40510.17610.33870.1229-0.31750.1465-0.1875-0.08550.3456-0.02170.01920.57170.03650.1284-37.9267-17.33360.2892
312.3422-1.0427-3.03633.19892.86294.7567-0.0656-0.4486-0.1720.17710.2113-0.0157-0.1716-0.0471-0.13230.35290.0071-0.02790.6110.07750.212-35.679-26.50786.0823
324.8227-2.8171-3.9696.56257.31519.6743-0.246-0.1342-0.14050.10050.13070.6448-0.0769-0.166-0.00220.3412-0.04440.01020.47060.07040.2012-45.0903-28.82580.7506
331.3258-1.34070.02552.93760.37061.16490.0489-0.3869-0.23650.23590.13580.4352-0.20010.1581-0.12670.4522-0.03240.06460.65770.07750.1752-43.8972-17.73553.6734
340.36970.4435-0.58181.0536-0.4031.09480.38750.6494-0.1471-0.8965-0.54720.0491-0.0558-0.14540.08640.49370.010.01120.60720.00450.194-37.8004-24.209-12.654
357.1229-3.5202-5.58256.92254.42587.77891.07560.3605-0.08330.2392-0.92280.463-0.8238-1.6007-0.0690.52250.02730.05470.77120.03780.2344-52.1058-12.44634.3945
365.127-0.1666-0.70455.80662.5291.1890.26460.06070.48130.3992-0.1202-0.2352-0.75740.7518-0.17060.3155-0.0730.07850.57620.01460.2626-26.276-3.5368-9.9819
372.43911.7747-1.73479.77432.92733.38810.1946-0.4076-0.09220.4933-0.0572-0.90130.16840.1694-0.08640.3469-0.0110.01410.63160.07090.3156-20.3892-10.4203-7.2586
380.66680.5446-1.22321.43520.39584.38080.2111-0.41920.17870.2467-0.0454-0.3874-0.27160.49610.05240.44-0.06550.01350.71750.0169-0.0341-25.6261-17.5005-8.4621
395.30172.418-2.98724.57112.77666.6216-0.15131.36330.543-0.7971-0.38520.5725-0.1711-0.56740.39040.48270.044-0.0330.51660.08420.209-35.669-13.7908-13.5778
400.25510.82520.64973.16840.45876.67740.49181.04670.4015-0.5111-0.4404-0.51380.38060.69510.09370.54230.11190.16090.72770.08680.1927-20.6032-21.632-15.8388
410.70861.7494-1.35544.6937-3.28332.5915-0.32440.20990.0916-2.0150.31650.01480.45040.0454-0.00740.68290.0522-0.04010.73670.07560.2439-32.4383-14.4062-22.9018
421.2252-0.599-0.29691.72440.33280.28620.17830.120.0165-0.1608-0.0989-0.1257-0.11250.0318-0.07210.42910.00610.03010.64180.05150.1256-27.2143-12.1657-11.0765
432.8382-0.5836-0.65262.4258-0.21540.2331-0.0307-0.0157-0.1945-0.24020.0413-0.17870.71110.3961-0.09190.48160.0565-0.09810.5387-0.05620.2719-12.7455-45.5473-9.5152
441.0648-0.5078-2.04191.672-0.51178.1068-0.12090.5102-0.30760.0743-0.02430.0790.1309-0.19650.02920.34210.026-0.07080.54590.01370.1654-20.7416-41.2551-5.6881
451.2967-1.0971-0.11573.9213-0.21641.14360.15650.4317-0.2102-0.55320.03530.1759-0.0340.0363-0.19840.33470.0268-0.04960.4792-0.01720.2432-20.5976-37.9912-12.2055
461.82591.0796-1.12957.538-0.57610.6984-0.37151.222-0.1091-0.85250.0582-0.2527-0.60021.54810.24460.5665-0.04550.06021.01630.00720.2685-8.9239-37.8705-22.5907
476.1429-1.5567-3.12010.90120.05892.62920.2456-0.3678-0.05360.0564-0.0482-0.0617-0.25840.05-0.17930.4247-0.014-0.08240.55810.0050.1834-17.689-37.1462-0.8141
485.65863.7412.83512.9221.35162.0267-0.2981.4207-0.09-0.5878-0.1465-0.33190.53691.7730.43480.47780.18710.05630.83110.04470.4191-4.026-42.2525-16.4077
497.39284.20615.77086.11254.66495.03310.6956-0.7296-0.491.0927-0.3021-0.36260.11050.1274-0.36790.62090.0403-0.04610.57920.03490.1782-3.1508-54.575336.5484
501.12381.4541-1.0219.6071-0.6771.02990.0792-0.7944-0.21290.4987-0.066-1.556-0.16780.4321-0.04450.38850.094-0.15460.5618-0.03610.5613.5415-44.614832.323
514.1794.5494-1.47355.0268-1.47670.6875-0.108-0.3951-0.4555-0.0920.00960.06960.1163-0.05380.27870.42730.150.01080.4640.00450.3517-4.1969-58.717426.8329
521.2142-0.10530.53141.704-1.17561.1289-0.08480.29230.0208-0.0094-0.0668-0.2185-0.090.03120.16070.3710.03930.02780.4721-0.020.1965-2.9315-42.381826.9722
533.16612.0554-0.15181.4187-0.55624.37430.23780.5872-0.0146-0.0677-0.0273-0.1146-0.13440.2158-0.1910.41370.09180.06970.5368-0.01270.2912-0.2556-47.102217.7355
546.20547.6522-1.76819.575-2.1750.49310.2347-0.02350.04890.2615-0.1950.08210.00740.0788-0.02330.45670.11790.05040.5548-0.01350.21672.8723-54.489925.5129
551.79141.00231.83832.34711.98452.38140.0975-0.37660.0665-0.0898-0.1199-0.0368-0.11640.17570.05720.40450.10760.00840.46460.02790.22363.5669-43.313328.7054
564.6855-1.12631.45992.7525-0.18190.463-0.29170.2298-0.58140.44740.16250.39210.2720.4050.0840.52950.01880.07430.52240.010.2126-10.7681-52.976631.5217
574.67045.50653.5936.98294.43072.8430.6362-1.2612-0.19680.0426-0.5085-0.9042-0.8097-0.5821-0.15740.5875-0.0440.02430.63590.04730.330310.2055-40.717936.9829
582.75090.0012.14454.17270.90021.87650.1439-0.10530.1406-0.06-0.02330.1139-0.2473-0.2065-0.07320.35710.0932-0.02780.46710.03850.1977-19.6306-31.380333.1643
590.54170.43460.67913.83273.54243.595-0.10250.0198-0.034-0.2077-0.05790.1676-0.02920.13930.18840.34750.03910.01480.48510.0240.2037-19.6007-38.84824.0579
605.51610.71870.23260.9662-0.10970.01190.1209-0.73950.52940.1417-0.2214-0.28580.2938-0.02060.01540.4820.07910.01260.6707-0.02560.2298-14.4307-44.108935.5931
614.9363-5.27812.87125.644-3.18917.09050.86260.9557-0.6348-1.7366-0.79061.8358-0.5659-0.1116-0.10510.5250.0232-0.11320.5475-0.07140.4086-27.7352-45.45719.8576
628.55522.48664.74072.54170.9612.7240.3635-0.74410.22291.0955-0.21430.30010.329-0.8712-0.1260.6111-0.04540.0790.5120.0420.2641-23.1931-49.099934.6332
639.3031-0.62276.11491.51691.55456.62460.1518-0.5535-0.07680.00140.10040.15830.7788-1.2263-0.27850.3386-0.04730.05460.428-0.02420.4334-28.211-41.9632.373
648.2139-5.25845.3548.3295-7.51358.6451-0.1446-0.16590.2059-0.3402-0.1109-0.14210.4167-0.82830.17320.3847-0.0510.00680.3813-0.01360.2197-26.3405-35.343126.5381
650.34130.0934-0.06120.8181-0.25681.10670.1141-0.1302-0.05570.19180.07040.20890.27840.0275-0.06560.47590.09160.01870.7748-0.0048-0.081-17.8461-39.909135.0966
661.34610.0427-0.31343.94453.01123.681-0.1071-0.1671-0.05920.12120.3333-0.13690.00820.6564-0.19390.38530.0532-0.02940.50890.06750.1776-14.5078-40.458227.1802
676.61492.4501-4.22966.1665-1.36828.4605-0.11660.2159-1.538-0.572-0.0574-0.06941.1441-0.17930.11150.7324-0.0148-0.1860.51280.02660.3687-27.3887-62.80843.9623
688.9118-0.44976.29976.7748-4.76437.75260.0794-0.1641-0.267-0.13630.4090.08780.5075-0.1677-0.45610.4524-0.0399-0.01650.4523-0.04240.2484-23.0174-56.29498.8461
695.7278-2.06041.36647.8611.93762.14460.2503-0.2238-0.78180.30210.03620.2430.4848-0.0693-0.28340.5221-0.0282-0.07320.46010.06440.436-22.2895-62.642814.9711
707.0132-0.0153-2.80855.9096-4.27776.6345-0.19080.3643-0.1019-0.02870.2374-0.1238-0.0017-0.5128-0.06810.42540.0195-0.11140.3758-0.03930.2417-27.1345-56.63877.8247
713.01042.01621.91837.4864.60739.6705-0.13570.5799-0.0558-0.73740.9154-0.8584-0.0199-0.1397-0.70650.4042-0.07950.16760.5723-0.03720.468119.467-32.1439-16.8574
728.88542.06011.7486.03620.75782.8201-0.0821.0099-2.5641-0.37730.1997-0.4540.0814-0.1392-0.13930.45180.09020.19430.5635-0.1580.990412.703-45.2444-12.2937
735.317-4.7616-5.27335.66324.66955.27720.2275-0.71540.22070.19410.3946-0.7906-0.541.2108-0.67310.3741-0.0133-0.02450.5825-0.02490.565726.2958-27.9213-4.7627
741.11980.492.8852.6247-0.04738.0253-0.0558-0.3832-0.1380.08860.12980.0747-0.0207-0.5952-0.06440.30920.07790.07320.46940.07360.41659.2195-33.6191-3.279
750.77091.40140.77455.9646-0.39871.73970.1460.0118-0.2066-0.1299-0.0711-0.43440.11130.0876-0.07590.27070.08430.05450.43630.06130.350512.6283-38.9187-7.6093
767.32788.00313.24292.05992.85584.0488-0.33760.2974-1.2761-0.16810.5069-1.1125-0.0456-0.0347-0.2290.44650.0645-0.00740.5563-0.07910.593613.8829-32.0711-13.5735
776.0945-2.00163.10025.22460.38932.01670.1060.1781-0.1818-0.29230.26660.41980.4143-0.5516-0.32880.29050.09370.03990.3946-0.02630.2957-2.9846-15.3028-13.6153
782.05470.41441.35541.05890.56160.9642-0.0138-0.25010.0346-0.0418-0.0820.0702-0.2439-0.29940.13680.47060.09480.06890.56670.03730.2154.5431-15.595-4.3493
797.29584.1182.86076.68895.73755.3741-0.37740.30450.0049-0.44760.41370.0386-0.2350.5404-0.07610.53470.0430.0860.46530.06540.190810.9668-15.8228-10.8273
806.2872-5.96853.24978.97660.36675.3001-0.20560.64071.2887-1.1550.5256-1.16760.69010.2386-0.46410.5669-0.11070.19840.6985-0.02110.458713.8423-11.51-19.409
812.2960.1771.86220.77020.34245.2585-0.01950.1605-0.0516-0.26880.0444-0.0494-0.2797-0.1211-0.01080.41920.050.07020.48560.02510.19814.9152-15.9437-10.2836
824.70880.70861.79535.33241.71896.56570.0426-0.12680.20390.00260.5892-0.8155-0.25940.3106-0.55090.3393-0.00860.13140.5153-0.09080.470224.576-11.542412.8407
836.5783-0.06961.2374.4164-0.00070.48920.0760.9693-0.2006-0.21740.0608-0.9813-0.3160.4028-0.14010.45580.01240.15020.6432-0.0590.577827.2696-14.50712.5085
844.62872.781-1.70824.58771.12937.97930.24720.21830.5162-0.59120.4317-1.027-1.28880.1107-0.5680.584-0.09650.17280.5755-0.05620.685529.4251-4.61697.2764
853.8425-4.3899-0.41135.6609-1.61976.62890.44510.1701-0.74420.1212-0.36171.47340.1264-0.1587-0.0270.39630.07840.01620.6383-0.09750.628718.9609-18.245212.1023
866.99483.45482.13573.2828-2.42958.6516-0.3179-0.85370.3868-0.16150.21460.0132-0.22780.11410.08960.36120.01440.11390.5869-0.17620.641818.7616-16.061818.1691
875.8440.75912.36443.87855.27437.48811.5612-0.09022.3446-0.271-1.14892.7912-2.6094-0.4464-0.3721.0810.00140.19560.5672-0.18911.199928.70193.43813.8785
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 105 )
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 111 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 28 )
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 64 )
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 73 )
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 91 )
15X-RAY DIFFRACTION15chain 'B' and (resid 92 through 100 )
16X-RAY DIFFRACTION16chain 'B' and (resid 101 through 113 )
17X-RAY DIFFRACTION17chain 'B' and (resid 114 through 120 )
18X-RAY DIFFRACTION18chain 'C' and (resid 31 through 49 )
19X-RAY DIFFRACTION19chain 'C' and (resid 50 through 62 )
20X-RAY DIFFRACTION20chain 'C' and (resid 63 through 70 )
21X-RAY DIFFRACTION21chain 'C' and (resid 71 through 82 )
22X-RAY DIFFRACTION22chain 'C' and (resid 83 through 110 )
23X-RAY DIFFRACTION23chain 'C' and (resid 111 through 118 )
24X-RAY DIFFRACTION24chain 'C' and (resid 119 through 139 )
25X-RAY DIFFRACTION25chain 'C' and (resid 140 through 146 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 7 )
27X-RAY DIFFRACTION27chain 'D' and (resid 8 through 18 )
28X-RAY DIFFRACTION28chain 'D' and (resid 19 through 25 )
29X-RAY DIFFRACTION29chain 'D' and (resid 26 through 36 )
30X-RAY DIFFRACTION30chain 'D' and (resid 37 through 52 )
31X-RAY DIFFRACTION31chain 'D' and (resid 53 through 65 )
32X-RAY DIFFRACTION32chain 'D' and (resid 66 through 79 )
33X-RAY DIFFRACTION33chain 'D' and (resid 80 through 94 )
34X-RAY DIFFRACTION34chain 'D' and (resid 95 through 105 )
35X-RAY DIFFRACTION35chain 'D' and (resid 106 through 111 )
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 17 )
37X-RAY DIFFRACTION37chain 'E' and (resid 18 through 28 )
38X-RAY DIFFRACTION38chain 'E' and (resid 29 through 39 )
39X-RAY DIFFRACTION39chain 'E' and (resid 40 through 51 )
40X-RAY DIFFRACTION40chain 'E' and (resid 52 through 60 )
41X-RAY DIFFRACTION41chain 'E' and (resid 61 through 67 )
42X-RAY DIFFRACTION42chain 'E' and (resid 68 through 120 )
43X-RAY DIFFRACTION43chain 'F' and (resid 31 through 49 )
44X-RAY DIFFRACTION44chain 'F' and (resid 50 through 70 )
45X-RAY DIFFRACTION45chain 'F' and (resid 71 through 110 )
46X-RAY DIFFRACTION46chain 'F' and (resid 111 through 118 )
47X-RAY DIFFRACTION47chain 'F' and (resid 119 through 139 )
48X-RAY DIFFRACTION48chain 'F' and (resid 140 through 146 )
49X-RAY DIFFRACTION49chain 'G' and (resid 1 through 9 )
50X-RAY DIFFRACTION50chain 'G' and (resid 10 through 18 )
51X-RAY DIFFRACTION51chain 'G' and (resid 19 through 36 )
52X-RAY DIFFRACTION52chain 'G' and (resid 37 through 52 )
53X-RAY DIFFRACTION53chain 'G' and (resid 53 through 65 )
54X-RAY DIFFRACTION54chain 'G' and (resid 66 through 79 )
55X-RAY DIFFRACTION55chain 'G' and (resid 80 through 94 )
56X-RAY DIFFRACTION56chain 'G' and (resid 95 through 106 )
57X-RAY DIFFRACTION57chain 'G' and (resid 107 through 111 )
58X-RAY DIFFRACTION58chain 'H' and (resid 1 through 17 )
59X-RAY DIFFRACTION59chain 'H' and (resid 18 through 39 )
60X-RAY DIFFRACTION60chain 'H' and (resid 40 through 51 )
61X-RAY DIFFRACTION61chain 'H' and (resid 52 through 57 )
62X-RAY DIFFRACTION62chain 'H' and (resid 58 through 64 )
63X-RAY DIFFRACTION63chain 'H' and (resid 65 through 73 )
64X-RAY DIFFRACTION64chain 'H' and (resid 74 through 83 )
65X-RAY DIFFRACTION65chain 'H' and (resid 84 through 100 )
66X-RAY DIFFRACTION66chain 'H' and (resid 101 through 120 )
67X-RAY DIFFRACTION67chain 'I' and (resid 31 through 49 )
68X-RAY DIFFRACTION68chain 'I' and (resid 50 through 82 )
69X-RAY DIFFRACTION69chain 'I' and (resid 83 through 110 )
70X-RAY DIFFRACTION70chain 'I' and (resid 111 through 146 )
71X-RAY DIFFRACTION71chain 'J' and (resid 1 through 9 )
72X-RAY DIFFRACTION72chain 'J' and (resid 10 through 24 )
73X-RAY DIFFRACTION73chain 'J' and (resid 25 through 36 )
74X-RAY DIFFRACTION74chain 'J' and (resid 37 through 65 )
75X-RAY DIFFRACTION75chain 'J' and (resid 66 through 94 )
76X-RAY DIFFRACTION76chain 'J' and (resid 95 through 111 )
77X-RAY DIFFRACTION77chain 'K' and (resid 1 through 17 )
78X-RAY DIFFRACTION78chain 'K' and (resid 18 through 39 )
79X-RAY DIFFRACTION79chain 'K' and (resid 40 through 60 )
80X-RAY DIFFRACTION80chain 'K' and (resid 61 through 67 )
81X-RAY DIFFRACTION81chain 'K' and (resid 68 through 120 )
82X-RAY DIFFRACTION82chain 'L' and (resid 31 through 82 )
83X-RAY DIFFRACTION83chain 'L' and (resid 83 through 104 )
84X-RAY DIFFRACTION84chain 'L' and (resid 105 through 118 )
85X-RAY DIFFRACTION85chain 'L' and (resid 119 through 132 )
86X-RAY DIFFRACTION86chain 'L' and (resid 133 through 139 )
87X-RAY DIFFRACTION87chain 'L' and (resid 140 through 146 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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