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- PDB-4zbi: Mcl-1 complexed with small molecules -

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基本情報

登録情報
データベース: PDB / ID: 4zbi
タイトルMcl-1 complexed with small molecules
要素Induced myeloid leukemia cell differentiation protein Mcl-1
キーワードapoptosis/apoptosis inhibitor / Inhibitor / Complex / apoptosis-apoptosis inhibitor complex
機能・相同性
機能・相同性情報


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
類似検索 - 分子機能
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-4M6 / Induced myeloid leukemia cell differentiation protein Mcl-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 / 解像度: 2.5 Å
データ登録者Zhao, B.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: J.Med.Chem. / 年: 2015
タイトル: Discovery of tricyclic indoles that potently inhibit mcl-1 using fragment-based methods and structure-based design.
著者: Burke, J.P. / Bian, Z. / Shaw, S. / Zhao, B. / Goodwin, C.M. / Belmar, J. / Browning, C.F. / Vigil, D. / Friberg, A. / Camper, D.V. / Rossanese, O.W. / Lee, T. / Olejniczak, E.T. / Fesik, S.W.
履歴
登録2015年4月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年4月29日Provider: repository / タイプ: Initial release
改定 1.12015年5月27日Group: Database references
改定 1.22017年9月27日Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
改定 1.32019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
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: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Induced myeloid leukemia cell differentiation protein Mcl-1
E: Induced myeloid leukemia cell differentiation protein Mcl-1
F: Induced myeloid leukemia cell differentiation protein Mcl-1
G: Induced myeloid leukemia cell differentiation protein Mcl-1
H: Induced myeloid leukemia cell differentiation protein Mcl-1
I: Induced myeloid leukemia cell differentiation protein Mcl-1
J: Induced myeloid leukemia cell differentiation protein Mcl-1
K: Induced myeloid leukemia cell differentiation protein Mcl-1
L: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)218,82924
ポリマ－214,20312
非ポリマー4,62512
水3,189177
1
A: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
5
E: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
6
F: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
7
G: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
8
H: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
9
I: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
10
J: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
11
K: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
12
L: Induced myeloid leukemia cell differentiation protein Mcl-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2362
ポリマ－17,8501
非ポリマー3851
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)62.256, 134.015, 135.931
Angle α, β, γ (deg.)90.00, 99.65, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


分子量: 17850.281 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MCL1, BCL2L3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q07820
#2: 化合物
ChemComp-4M6 / 1-[3-(naphthalen-1-yloxy)propyl]-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinoline-2-carboxylic acid


分子量: 385.455 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C25H23NO3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 177 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 2.61 Å3/Da / 溶媒含有率: 52.87 %
結晶化手法: 蒸発脱水法 / 詳細: PEG3350, magnesium chloride, Bis-Tris / PH範囲: 6.0-8.0

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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: APS / ビームライン: 21-ID-D / 波長: 1.07816 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2012年7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: 1.07816 Å / 相対比: 1
反射解像度: 2.5→50 Å / Num. obs: 68726 / % possible obs: 90.7 % / 冗長度: 2.7 % / Rmerge(I) obs: 0.06 / Rsym value: 0.049 / Net I/σ(I): 17.3
反射 シェル解像度: 2.5→2.54 Å / 冗長度: 2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 82.4

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_1951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
精密化解像度: 2.5→29.966 Å / SU ML: 0.36 / 交差検証法: THROUGHOUT / σ(F): 1.44 / 位相誤差: 25.81 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2395 1988 2.89 %
Rwork0.1816 --
obs0.1833 68687 90.4 %
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: 2.5→29.966 Å
タンパク質核酸リガンド溶媒全体
原子数14484 0 348 177 15009
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0115116
X-RAY DIFFRACTIONf_angle_d1.41120370
X-RAY DIFFRACTIONf_dihedral_angle_d18.0545678
X-RAY DIFFRACTIONf_chiral_restr0.0662208
X-RAY DIFFRACTIONf_plane_restr0.0082582
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56170.36411060.26614085X-RAY DIFFRACTION78
2.5617-2.6310.33921450.25964433X-RAY DIFFRACTION84
2.631-2.70830.3241290.23854508X-RAY DIFFRACTION86
2.7083-2.79570.3031360.2344599X-RAY DIFFRACTION87
2.7957-2.89550.2921440.22874724X-RAY DIFFRACTION90
2.8955-3.01140.30621360.23484742X-RAY DIFFRACTION91
3.0114-3.14830.28821500.22814924X-RAY DIFFRACTION93
3.1483-3.31410.26461430.22014929X-RAY DIFFRACTION93
3.3141-3.52140.30221460.21024997X-RAY DIFFRACTION94
3.5214-3.79280.24451330.19014221X-RAY DIFFRACTION80
3.7928-4.17360.211460.15384883X-RAY DIFFRACTION93
4.1736-4.77540.18541520.14035185X-RAY DIFFRACTION98
4.7754-6.00850.21341580.15175189X-RAY DIFFRACTION98
6.0085-300.16521640.12855280X-RAY DIFFRACTION98
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)
12.3099-2.7008-3.03726.26693.21224.33460.0190.337-0.9216-0.34520.20030.79040.1545-0.297-0.09850.1853-0.0723-0.02470.35350.03990.3285-9.8519-34.1474-7.8496
22.76290.3468-3.3311.25951.61747.6089-0.6921-0.3941-0.5296-0.3320.44-0.93291.01750.9648-0.27320.74020.1198-0.06951.2918-0.18611.2115-15.3342-39.4767-13.3058
32.94830.32320.41211.7471-0.22482.2832-0.05960.00090.18230.01050.15130.4388-0.2033-0.323-0.01110.27090.02260.04140.39840.06820.3998-11.2459-23.297-0.7784
41.9927-1.47370.27584.7337-2.84593.9763-0.0348-0.0612-0.0103-0.29610.0519-0.09560.0891-0.1511-0.03710.2567-0.02850.03130.31970.07060.3109-4.3095-30.108-3.1651
50.01760.04320.12560.11460.32410.89790.1232-0.7538-0.84620.3998-0.03360.62180.8256-0.66130.2650.3034-0.0340.09610.55330.23040.5356-15.5082-40.28935.5963
63.18142.6083-0.10653.3133-1.74412.4761-0.2059-0.0720.3019-0.11510.0002-0.54880.03760.64820.21630.32150.015-0.03310.3518-0.01750.228318.8708-0.21272.4951
72.18610.34181.33681.1508-2.52987.6332-0.11780.65350.9124-0.57470.0477-0.1062-1.7641-0.02140.281.05060.0777-0.16911.22480.12011.001726.95053.90763.4359
80.97530.28840.51842.18160.29261.7722-0.1376-0.05720.0057-0.08260.041-0.03040.01110.1788-0.02860.34020.00810.04720.38660.03290.274612.014-9.6748.027
91.7115-1.39860.11543.8454-0.65842.09390.06810.04030.0013-0.096-0.1822-0.1035-0.06490.0186-0.00810.3183-0.02580.00770.3580.0050.225111.1007-5.1594.5433
100.3606-0.4043-0.22771.7515-1.13511.6041-0.409-0.77130.29450.36910.1243-0.8321-0.05630.6982-0.05440.51550.0165-0.01260.4228-0.0160.250211.69467.67514.4731
115.9828-3.9828-0.49864.2554-0.25873.007-0.2587-0.53860.26940.4082-0.2341-0.64330.22790.4798-0.05840.3085-0.0074-0.01750.41460.15920.280219.8044-37.33632.3711
123.202-1.1097-3.40190.37841.17653.618-0.4645-0.2721-0.3610.3639-0.9231.09120.2719-0.63560.44231.149-0.04160.15371.208-0.02811.536824.4076-36.19810.7106
132.99681.160.7314.2698-2.69572.51010.1376-0.0345-0.12120.0492-1.198-0.8458-0.16710.9869-0.46970.38620.08050.0110.64940.39710.493626.0305-47.33431.5683
144.4929-2.10160.50823.79651.19613.5147-0.11190.2808-0.1774-0.1843-0.2439-0.44360.65860.55720.39170.61560.43820.5350.90950.38160.086228.8874-41.3307-17.8668
154.45691.02680.59041.34920.1341.0795-0.5360.06150.7581-0.15640.07320.27870.14790.1674-0.07730.44380.11690.07770.30850.2190.20119.0827-32.4061-15.6067
160.90280.3396-0.51022.3348-0.26841.5037-0.20880.4221-0.3388-0.4913-0.8374-0.28040.56940.0312-0.1588-0.26930.8622-0.2055-0.02230.67480.293322.3593-42.5631-9.4466
173.11330.9245-2.21012.5739-0.98731.56450.32040.17450.32620.3135-0.20670.3488-0.138-0.0296-0.030.26710.0484-0.01570.390.10360.287815.5246-37.9375-4.786
185.3142-1.01240.80282.63762.81183.70960.3242-0.4051-0.81710.4250.04650.23330.84130.20270.30250.36840.05190.05940.55070.21930.385218.2501-52.78323.2855
192.3583-2.6953-1.35728.1225-0.243.9694-0.0045-0.1125-0.56930.07740.18680.6984-0.0152-0.2847-0.29140.1998-0.0344-0.0380.24760.04470.167837.0963-3.2072-58.1109
202.2798-2.3909-3.88663.90884.5916.8044-0.5794-0.3409-0.29280.3628-0.13090.58830.0102-1.21490.04970.5439-0.00890.10990.61240.13580.492531.9345-6.7992-51.8337
211.1814-0.25560.03941.0773-0.6312.49730.12080.12220.0675-0.1835-0.00290.1166-0.1424-0.21080.01040.32590.0359-0.02370.33910.05010.226336.79626.8415-66.2751
222.264-0.09260.93911.33040.28132.8858-0.03730.2246-0.0637-0.1350.04020.0937-0.0753-0.0430.01450.32890.03020.02260.26020.0690.259338.01443.208-65.9733
232.0526-0.64740.23012.63130.16571.6447-0.2797-0.64810.02890.40130.29990.0966-0.30990.3598-0.04020.35090.0085-0.01270.38230.04850.229146.91155.9543-50.6086
243.3538-0.5006-0.25026.80440.32211.26340.43030.0995-0.08850.5526-0.4585-0.50120.05830.4767-0.12150.27310.03880.00520.38760.1350.177233.6282-17.6712-28.0815
251.87050.8349-1.27330.3758-0.57090.8701-0.90950.7572-0.2241-2.0699-0.75510.4701-0.3586-0.17510.67251.09050.1263-0.1640.9201-0.03530.879841.1848-22.7561-26.8259
261.8637-0.4765-0.89710.97450.36532.2117-0.0646-0.06580.10840.5192-0.00880.0106-0.34050.2404-0.01280.44790.03810.01850.42880.09430.286228.927-5.8564-25.7876
271.44190.126-0.11312.0429-0.15823.55530.0072-0.06460.03140.3523-0.07460.224-0.2293-0.04310.00970.34490.0440.04480.34310.06490.202127.4606-10.4263-29.2722
284.47070.3536-2.48020.3014-0.12441.6887-0.12330.3918-0.0959-0.3087-0.1303-0.35490.18120.86550.08090.30930.03810.03490.42440.06040.192339.626-11.0576-41.5269
293.6387-2.44640.58764.4863-3.23855.03070.13510.229-0.4184-0.12070.06930.22340.3603-0.9668-0.18370.27170.02930.02840.3727-0.04630.242-5.69093.4976-16.8201
302.4101-0.1756-1.03660.5412-1.29665.0187-0.377-1.27050.21670.3295-0.0822-0.02820.5879-0.65280.10270.80810.0305-0.01711.36630.03211.0492-14.70344.6303-15.0531
312.1214-0.2240.41951.13440.03541.2718-0.19740.5182-0.4585-0.5204-0.0117-0.0589-0.1484-0.30.01280.39770.02460.08330.4861-0.060.37071.71533.019-27.6137
321.5680.75390.45133.14640.72242.3913-0.23730.606-0.4424-0.61160.2946-0.3853-0.2901-0.0427-0.06340.3118-0.0090.05930.4283-0.0940.26723.03025.2918-26.4831
331.30891.48671.09353.71762.6344.31270.09790.3657-0.86250.53790.0095-0.32610.8505-0.1547-0.03320.3319-0.02970.05580.4027-0.1020.39420.429-3.39-20.3335
341.63411.52950.1271.4481-0.19044.92180.0656-0.2190.35140.18580.1096-0.2647-0.5872-0.58140.04960.49610.1014-0.02680.30040.02220.30721.826516.3852-14.7279
354.8127-2.98511.34716.4655-1.76344.65440.4018-0.9982-0.55890.24650.01060.4462-0.0486-0.6056-0.17810.3928-0.01450.0470.3213-0.020.154734.0169-56.5636-34.023
362.0007-0.52415.49953.24094.14568.8638-1.146-0.80330.66480.5182-1.1883-0.5712-0.71490.6205-0.20650.69810.04880.18151.29080.45570.720629.3841-57.4669-26.1365
372.69960.32080.73483.07011.27672.8020.284-0.15290.3667-0.19130.06330.1712-0.8201-1.09440.12330.5180.1460.09910.4764-0.02650.291328.4344-48.2029-42.9451
381.9936-0.98080.2050.9548-0.57592.6812-0.18310.087-0.3057-0.60530.09690.1627-0.084-0.20920.02680.3768-0.00170.00480.2909-0.05490.266233.1787-56.6853-48.4253
394.93983.621.20294.37841.1222.28390.3610.2661-0.33650.4378-0.0924-0.13060.11770.1589-0.00930.3574-0.0220.00940.27120.00580.232640.373-56.8622-40.6792
401.3554-2.047-0.93425.31650.33051.1518-0.0853-0.70880.83911.19390.0421-0.4511-0.9427-0.2450.05460.9681-0.0650.0656-0.2072-0.6853-0.174239.0122-41.2705-32.7488
412.33752.66091.0898.6135-1.96222.70090.4496-0.06930.51290.3277-0.11610.94010.1284-0.4587-0.18570.21550.11350.07840.33860.02820.28985.9708-24.8817-39.5012
420.94-1.437-1.03442.21051.40924.637-1.362-0.4631-1.1909-0.54840.11470.51210.6079-0.6213-0.46190.53810.05870.00020.82270.18290.6531.3057-20.7677-45.9413
433.38081.0034-1.24364.0357-3.86938.1178-0.19460.073-0.6073-0.9631-0.08670.07611.2194-0.7926-0.17540.43-0.0669-0.01090.30580.05160.46763.6952-35.3786-44.7313
442.9370.2572-0.07262.21870.00642.5694-0.2063-0.4672-0.07290.3380.20020.18970.4017-0.20730.02670.43850.06070.14560.38050.1210.21997.8313-35.2508-23.6664
452.57270.3857-1.04542.2080.59132.7902-0.0252-0.3015-0.12740.25640.11410.14050.2469-0.20450.02350.33570.05860.03570.39420.12010.26647.5121-31.6754-31.8033
463.080.72350.20052.1078-0.67261.6101-0.29660.2145-0.3432-0.7460.2877-0.00380.40130.1028-0.04610.4180.08510.02120.3161-0.01820.268216.7459-33.1465-46.5618
473.8514-3.07861.3598.5235-0.67420.77750.28860.17050.077-1.0117-0.2359-0.538-0.27120.5247-0.05640.30530.010.02460.45390.06430.24122.9317-9.3019-69.296
487.89941.16432.36291.35921.71732.2999-1.2663-0.79871.41841.65351.2773-0.27111.03562.0676-0.69281.0663-0.1590.14480.94060.02080.988810.5655-4.4649-70.3431
492.41540.83550.34991.18670.40791.99830.00920.2433-0.1441-0.2698-0.04-0.10690.28620.3477-0.02560.45180.07090.03110.47870.06440.3145-1.2315-21.2979-71.862
501.3984-0.0470.68421.30780.23272.32730.09280.3557-0.0727-0.4196-0.0478-0.0438-0.1359-0.1965-0.0130.43380.0825-0.02110.3920.02440.22-2.7792-17.6825-71.724
516.00451.2607-3.20312.08510.93153.67850.0929-0.2874-0.23080.46940.0907-0.03560.16360.7196-0.03750.2958-0.0133-0.06940.36950.05630.2674-4.3123-12.9386-53.9969
520.63090.3524-0.1710.3217-0.29160.86280.14190.13590.24350.1669-0.1228-0.171-0.15470.05040.03390.29390.049-0.03420.33360.03350.37917.7613-15.8875-56.2455
534.6775-0.76562.45795.6808-3.06135.33810.03530.05850.1744-1.01620.0618-1.0143-0.08320.88490.12860.2652-0.13260.02120.50390.00650.23910.6418-64.7817-41.7677
543.77160.44032.79030.05180.32532.0584-1.4026-1.22930.87191.42850.62-0.3064-1.2601-0.4388-0.52691.176-0.1030.42991.0436-0.16981.25148.4748-61.8666-46.319
552.9111-0.07710.10881.19371.79212.70670.01070.125-0.2323-0.17070.3826-1.1311-0.07030.85270.17110.2511-0.09570.03141.06180.0630.4178.905-68.0325-33.6644
565.30430.21775.1971.83870.48269.2748-0.1267-0.2614-0.8882-0.0529-0.2242-0.64250.998-0.2201-0.25940.40670.01080.03540.46780.07130.366-4.0833-85.1507-35.5096
571.5190.76130.18741.66430.3620.3177-0.01730.0877-0.1439-0.1094-0.0105-0.050.1150.32880.00790.2778-0.0195-0.05260.4760.01250.1804-6.004-75.2321-35.0883
580.210.73790.54613.28690.99313.4867-0.12470.3668-0.3478-1.1176-0.0940.1978-0.34810.03760.00740.3906-0.01670.00980.5227-0.02980.3099-5.9934-71.8771-42.9051
592.4026-0.78191.98052.93781.08382.72830.20910.05030.060.71050.135-0.5392-0.13980.43870.0930.1636-0.4297-0.17680.272-0.12390.1631-6.0889-58.299-27.2486
600.2274-0.5481-0.49671.36581.23821.2006-0.13680.20720.41320.361-0.0904-1.1397-0.69270.49910.49030.0714-0.2741-0.39160.77690.09660.26876.7603-60.43-27.6646
613.2629-1.4822-1.68644.3585-3.14816.0585-0.3524-0.4037-0.6453-0.0816-0.2944-0.91160.6781.14190.31790.4920.12540.09130.38870.05990.417432.764-28.541835.093
621.9408-1.15221.61920.9514-0.58253.0875-0.1405-0.3449-0.14320.4931-0.54210.11990.6323-0.43130.56141.04370.2690.02071.42260.23291.275140.5713-32.496135.9383
632.0821-1.3889-0.97987.33030.35140.8115-0.32060.461-0.431-0.3599-0.2402-0.20510.4670.07510.12880.51740.0720.09830.55090.0180.388630.7472-23.450322.7547
642.0821-0.1205-0.842.3396-0.67762.4529-0.1695-0.10520.06260.0409-0.04190.05040.40040.03780.00520.4136-0.001-0.00010.39340.0110.252424.4765-20.956731.9676
655.39452.32633.41614.6155-2.28767.0913-0.41050.1437-1.1881-0.89440.031-0.15650.61080.33480.0761.20050.05110.3570.39010.00690.627927.4932-38.240524.637
661.4710.62961.41354.2-4.01247.8734-0.20410.0678-0.111-0.2340.09210.69960.1895-0.8794-0.13280.4795-0.0283-0.05510.25530.02030.362728.044-32.7675-83.0403
674.5968-2.2155-3.73352.53990.92953.5172-0.7771.1283-1.1475-0.6090.1247-0.20372.3586-0.12970.44930.94740.0714-0.0941.2117-0.07131.10319.2819-34.198-84.9777
681.80480.0667-1.69464.37482.94194.62940.1576-0.074-0.1050.5105-0.22880.6130.1175-0.92010.04030.6212-0.07490.12330.4158-0.00440.359126.3766-41.7218-75.1648
691.90330.0418-0.82492.0671-0.662.12820.1147-0.51460.30280.16070.12680.16170.106-0.2859-0.01810.61210.0121-0.0430.4032-0.0190.306639.0595-25.2555-69.0511
702.27680.9506-0.79422.75020.2362.8473-0.05740.0401-0.0417-0.1131-0.0952-0.05510.0023-0.13590.03960.50710.00260.02940.26570.0460.31135.9455-32.4564-77.3402
713.2325-0.8237-0.05164.0671-0.38365.3982-0.31860.3376-0.345-0.2101-0.05270.45790.6505-0.4701-0.02230.88010.04420.22810.0401-0.18170.450831.6039-47.6427-80.8905
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 280 )
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 322 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 191 )
7X-RAY DIFFRACTION7chain 'B' and (resid 192 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 255 )
9X-RAY DIFFRACTION9chain 'B' and (resid 256 through 310 )
10X-RAY DIFFRACTION10chain 'B' and (resid 311 through 323 )
11X-RAY DIFFRACTION11chain 'C' and (resid 171 through 191 )
12X-RAY DIFFRACTION12chain 'C' and (resid 192 through 202 )
13X-RAY DIFFRACTION13chain 'C' and (resid 203 through 223 )
14X-RAY DIFFRACTION14chain 'C' and (resid 224 through 235 )
15X-RAY DIFFRACTION15chain 'C' and (resid 236 through 254 )
16X-RAY DIFFRACTION16chain 'C' and (resid 255 through 280 )
17X-RAY DIFFRACTION17chain 'C' and (resid 281 through 310 )
18X-RAY DIFFRACTION18chain 'C' and (resid 311 through 321 )
19X-RAY DIFFRACTION19chain 'D' and (resid 171 through 191 )
20X-RAY DIFFRACTION20chain 'D' and (resid 192 through 202 )
21X-RAY DIFFRACTION21chain 'D' and (resid 203 through 255 )
22X-RAY DIFFRACTION22chain 'D' and (resid 256 through 301 )
23X-RAY DIFFRACTION23chain 'D' and (resid 302 through 322 )
24X-RAY DIFFRACTION24chain 'E' and (resid 171 through 191 )
25X-RAY DIFFRACTION25chain 'E' and (resid 192 through 202 )
26X-RAY DIFFRACTION26chain 'E' and (resid 203 through 254 )
27X-RAY DIFFRACTION27chain 'E' and (resid 255 through 310 )
28X-RAY DIFFRACTION28chain 'E' and (resid 311 through 322 )
29X-RAY DIFFRACTION29chain 'F' and (resid 171 through 191 )
30X-RAY DIFFRACTION30chain 'F' and (resid 192 through 202 )
31X-RAY DIFFRACTION31chain 'F' and (resid 203 through 254 )
32X-RAY DIFFRACTION32chain 'F' and (resid 255 through 280 )
33X-RAY DIFFRACTION33chain 'F' and (resid 281 through 301 )
34X-RAY DIFFRACTION34chain 'F' and (resid 302 through 321 )
35X-RAY DIFFRACTION35chain 'G' and (resid 171 through 191 )
36X-RAY DIFFRACTION36chain 'G' and (resid 192 through 202 )
37X-RAY DIFFRACTION37chain 'G' and (resid 203 through 235 )
38X-RAY DIFFRACTION38chain 'G' and (resid 236 through 283 )
39X-RAY DIFFRACTION39chain 'G' and (resid 284 through 308 )
40X-RAY DIFFRACTION40chain 'G' and (resid 309 through 322 )
41X-RAY DIFFRACTION41chain 'H' and (resid 171 through 191 )
42X-RAY DIFFRACTION42chain 'H' and (resid 192 through 202 )
43X-RAY DIFFRACTION43chain 'H' and (resid 203 through 223 )
44X-RAY DIFFRACTION44chain 'H' and (resid 224 through 254 )
45X-RAY DIFFRACTION45chain 'H' and (resid 255 through 301 )
46X-RAY DIFFRACTION46chain 'H' and (resid 302 through 321 )
47X-RAY DIFFRACTION47chain 'I' and (resid 171 through 191 )
48X-RAY DIFFRACTION48chain 'I' and (resid 192 through 202 )
49X-RAY DIFFRACTION49chain 'I' and (resid 203 through 254 )
50X-RAY DIFFRACTION50chain 'I' and (resid 255 through 301 )
51X-RAY DIFFRACTION51chain 'I' and (resid 302 through 310 )
52X-RAY DIFFRACTION52chain 'I' and (resid 311 through 321 )
53X-RAY DIFFRACTION53chain 'J' and (resid 171 through 191 )
54X-RAY DIFFRACTION54chain 'J' and (resid 192 through 202 )
55X-RAY DIFFRACTION55chain 'J' and (resid 203 through 223 )
56X-RAY DIFFRACTION56chain 'J' and (resid 224 through 239 )
57X-RAY DIFFRACTION57chain 'J' and (resid 240 through 280 )
58X-RAY DIFFRACTION58chain 'J' and (resid 281 through 301 )
59X-RAY DIFFRACTION59chain 'J' and (resid 302 through 310 )
60X-RAY DIFFRACTION60chain 'J' and (resid 311 through 322 )
61X-RAY DIFFRACTION61chain 'K' and (resid 171 through 191 )
62X-RAY DIFFRACTION62chain 'K' and (resid 192 through 202 )
63X-RAY DIFFRACTION63chain 'K' and (resid 203 through 235 )
64X-RAY DIFFRACTION64chain 'K' and (resid 236 through 310 )
65X-RAY DIFFRACTION65chain 'K' and (resid 311 through 320 )
66X-RAY DIFFRACTION66chain 'L' and (resid 171 through 191 )
67X-RAY DIFFRACTION67chain 'L' and (resid 192 through 202 )
68X-RAY DIFFRACTION68chain 'L' and (resid 203 through 223 )
69X-RAY DIFFRACTION69chain 'L' and (resid 224 through 254 )
70X-RAY DIFFRACTION70chain 'L' and (resid 255 through 310 )
71X-RAY DIFFRACTION71chain 'L' and (resid 311 through 321 )

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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