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- PDB-5try: Structure of Mycobacterium tuberculosis proteasome in complex wit... -

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基本情報

登録情報
データベース: PDB / ID: 5try
タイトルStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2206
要素
  • Proteasome subunit alphaプロテアソーム
  • Proteasome subunit betaプロテアソーム
キーワードHYDROLASE/HYDROLASE inhibitor / N / C-capped dipeptides / Mycobacterium tuberculosis (結核菌) / proteasome (プロテアソーム) / inhibitors / HYDROLASE-HYDROLASE inhibitor complex
機能・相同性
機能・相同性情報


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / 細胞膜 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
(2~{S})-~{N}-[(2~{S})-3-methoxy-1-(naphthalen-1-ylmethylamino)-1-oxidanylidene-propan-2-yl]-4-oxidanylidene-2-(3-phenylpropanoylamino)-4-piperidin-1-yl-butanamide / Chem-7J0 / Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha
類似検索 - 構成要素
生物種Mycobacterium tuberculosis (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.00000818194 Å
データ登録者Hsu, H.-C. / Fan, H. / Singh, P.K. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070285 米国
引用ジャーナル: Biochemistry / 年: 2017
タイトル: Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.
著者: Hsu, H.C. / Singh, P.K. / Fan, H. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
履歴
登録2016年10月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年1月11日Provider: repository / タイプ: Initial release
改定 1.12017年1月18日Group: Database references
改定 1.22017年8月23日Group: Data collection / Refinement description / カテゴリ: diffrn_detector / software / Item: _diffrn_detector.detector / _software.name
改定 1.32017年9月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4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

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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: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit alpha
Q: Proteasome subunit alpha
R: Proteasome subunit alpha
S: Proteasome subunit alpha
T: Proteasome subunit alpha
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)725,46542
ポリマ－717,44728
非ポリマー8,01814
水3,693205
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area85050 Å2
ΔGint-70 kcal/mol
Surface area220070 Å2
手法PISA
単位格子
Length a, b, c (Å)120.650, 197.481, 164.810
Angle α, β, γ (deg.)90.000, 103.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
12
22
32
42
52
62
72
82
92
102
112
122
132
142

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9
121(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A12 - 13
131(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A15 - 20
141(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A22 - 25
151(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A27 - 34
161(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A35
171(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
181(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
191(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1101(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1111(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1121(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1131(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
211(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9
221(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B12 - 13
231(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B15 - 20
241(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B22 - 25
251(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B27 - 34
261(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B35
271(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
281(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
291(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
2101(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
2111(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
2121(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
2131(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 235
311(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9
321(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C12 - 13
331(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C15 - 20
341(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C22 - 25
351(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C27 - 34
361(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C35
371(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
381(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
391(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
3101(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
3111(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
3121(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
3131(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 235
411(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9
421(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D12 - 13
431(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D15 - 20
441(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D22 - 25
451(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D27 - 34
461(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D35
471(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
481(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
491(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4101(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4111(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4121(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4131(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
511(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9
521(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E12 - 13
531(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E15 - 20
541(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E22 - 25
551(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E27 - 34
561(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E35
571(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
581(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
591(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5101(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5111(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5121(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5131(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
611(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9
621(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F12 - 13
631(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F15 - 20
641(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F22 - 25
651(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F27 - 34
661(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F35
671(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
681(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
691(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
6101(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
6111(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
6121(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
6131(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 236
711(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9
721(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G12 - 13
731(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G15 - 20
741(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G22 - 25
751(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G27 - 34
761(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G35
771(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
781(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
791(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
7101(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
7111(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
7121(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
7131(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 235
811(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9
821(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O12 - 13
831(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O15 - 20
841(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O22 - 25
851(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O27 - 34
861(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O35
871(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
881(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
891(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8101(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8111(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8121(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8131(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
911(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9
921(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P12 - 13
931(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P15 - 20
941(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P22 - 25
951(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P27 - 34
961(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P35
971(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
981(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
991(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9101(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9111(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9121(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9131(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
1011(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9
1021(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q12 - 13
1031(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q15 - 20
1041(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q22 - 25
1051(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q27 - 34
1061(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q35
1071(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
1081(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
1091(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10101(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10111(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10121(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10131(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
1111(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9
1121(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R12 - 13
1131(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R15 - 20
1141(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R22 - 25
1151(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R27 - 34
1161(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R35
1171(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
1181(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
1191(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11101(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11111(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11121(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11131(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
1211(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9
1221(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S12 - 13
1231(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S15 - 20
1241(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S22 - 25
1251(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S27 - 34
1261(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S35
1271(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
1281(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
1291(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12101(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12111(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12121(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12131(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
1311(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9
1321(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T12 - 13
1331(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T15 - 20
1341(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T22 - 25
1351(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T27 - 34
1361(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T35
1371(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
1381(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
1391(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
13101(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
13111(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
13121(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
13131(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 235
1411(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9
1421(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U12 - 13
1431(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U15 - 20
1441(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U22 - 25
1451(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U27 - 34
1461(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U35
1471(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
1481(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
1491(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14101(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14111(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14121(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14131(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
112(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 7
122(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N8
132(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
142(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
152(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
162(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
172(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
182(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
192(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
212(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 7
222(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H8
232(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
242(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
252(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
262(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
272(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
282(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
292(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
312(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 7
322(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I8
332(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
342(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
352(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
362(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
372(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
382(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
392(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
412(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 7
422(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J8
432(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
442(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
452(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
462(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
472(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
482(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
492(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
512(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 7
522(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K8
532(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
542(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
552(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
562(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
572(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
582(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
592(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
612(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 7
622(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L8
632(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
642(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
652(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
662(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
672(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
682(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
692(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
712(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 7
722(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M8
732(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
742(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
752(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
762(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
772(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
782(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
792(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
812(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 7
822(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V8
832(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
842(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
852(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
862(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
872(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
882(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
892(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
912(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 7
922(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W8
932(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
942(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
952(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
962(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
972(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
982(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
992(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
1012(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 7
1022(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X8
1032(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1042(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1052(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1062(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1072(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1082(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1092(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1112(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 7
1122(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y8
1132(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1142(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1152(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1162(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1172(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1182(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1192(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1212(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 7
1222(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z8
1232(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1242(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1252(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1262(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1272(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1282(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1292(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1312(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A1 - 7
1322(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A8
1332(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1342(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1352(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1362(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1372(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1382(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1392(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1412(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B1 - 7
1422(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B8
1432(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1442(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1452(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1462(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1472(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1482(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235
1492(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 235

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Proteasome subunit alpha / プロテアソーム / 20S proteasome alpha subunit / Proteasome core protein PrcA


分子量: 25971.975 Da / 分子数: 14 / 断片: UNP residues 10-248 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (結核菌)
遺伝子: prcA, MRA_2124 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A5U4D5, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: タンパク質
Proteasome subunit beta / プロテアソーム / 20S proteasome beta subunit / Proteasome core protein PrcB


分子量: 25274.264 Da / 分子数: 14 / 断片: UNP residues 58-291 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (結核菌)
遺伝子: prcB, MRA_2125 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A5U4D6, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: 化合物
ChemComp-7J0 / (2~{S})-~{N}-[(2~{S})-3-methoxy-1-(naphthalen-1-ylmethylamino)-1-oxidanylidene-propan-2-yl]-4-oxidanylidene-2-(3-phenylpropanoylamino)-4-piperidin-1-yl-butanamide


タイプ: Non-polymer / クラス: 阻害剤 / 分子量: 572.694 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C33H40N4O5
参照: (2~{S})-~{N}-[(2~{S})-3-methoxy-1-(naphthalen-1-ylmethylamino)-1-oxidanylidene-propan-2-yl]-4-oxidanylidene-2-(3-phenylpropanoylamino)-4-piperidin-1-yl-butanamide
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 205 / 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 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.67 Å3/Da / 溶媒含有率: 53.86 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2 / 詳細: 60 mM sodium citrate (pH 6.2), 14% PEG-3350

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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: NSLS / ビームライン: X25 / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年9月15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: 1.1 Å / 相対比: 1
反射解像度: 3→51.0940207659 Å / Num. obs: 149567 / % possible obs: 99.3 % / 冗長度: 3.1 % / Biso Wilson estimate: 42.6433553783 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.1062 / Net I/σ(I): 6
反射 シェル解像度: 3→3.1 Å / 冗長度: 3 % / Rmerge(I) obs: 0.4539 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.695 / % possible all: 94.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155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
開始モデル: 3HFA

3hfa


解像度: 3.00000818194→51.0940207659 Å / SU ML: 0.392789617783 / 交差検証法: FREE R-VALUE / σ(F): 1.33648032855 / 位相誤差: 24.6665221358
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.233605050423 7373 4.93088204806 %
Rwork0.181585720234 142154 -
obs0.184197980489 149527 99.6720415414 %
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
原子変位パラメータBiso mean: 39.6209980062 Å2
精密化ステップサイクル: LAST / 解像度: 3.00000818194→51.0940207659 Å
タンパク質核酸リガンド溶媒全体
原子数46343 0 588 205 47136
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0030995915419847646
X-RAY DIFFRACTIONf_angle_d0.63417473449864445
X-RAY DIFFRACTIONf_chiral_restr0.0471691936477283
X-RAY DIFFRACTIONf_plane_restr0.004034630833838465
X-RAY DIFFRACTIONf_dihedral_angle_d15.494571451828456
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.3536353545912580.3019749027834713X-RAY DIFFRACTION99.5593831364
3.0341-3.06980.3666998880852710.2734923742794651X-RAY DIFFRACTION99.615462457
3.0698-3.10720.3246073047332490.2642123674494720X-RAY DIFFRACTION99.6390615601
3.1072-3.14650.2948858292752780.2489293527564695X-RAY DIFFRACTION99.5396317054
3.1465-3.18790.3206099356622320.2397994674514737X-RAY DIFFRACTION99.5991180597
3.1879-3.23160.3433693830632140.2388211776464732X-RAY DIFFRACTION99.3172690763
3.2316-3.27780.29023670682550.2337206524054697X-RAY DIFFRACTION99.4577224342
3.2778-3.32670.3042951427032330.2310949183944724X-RAY DIFFRACTION99.5581442057
3.3267-3.37870.2872977029172530.2146288176454726X-RAY DIFFRACTION99.6996395675
3.3787-3.4340.278803047682680.2220196689254753X-RAY DIFFRACTION99.7813990461
3.434-3.49320.2781368416832460.2025277999634709X-RAY DIFFRACTION99.6180136711
3.4932-3.55670.27000484992370.2045995886564747X-RAY DIFFRACTION99.5207667732
3.5567-3.62510.2737525134582680.2061278074454696X-RAY DIFFRACTION99.7187625552
3.6251-3.69910.2605701185222280.2065477555354715X-RAY DIFFRACTION99.6371699254
3.6991-3.77950.2424809862132440.1873407347244767X-RAY DIFFRACTION99.6817187189
3.7795-3.86740.2349666918742300.1837950324784692X-RAY DIFFRACTION99.7770119603
3.8674-3.96410.2624975132312540.1816884345984730X-RAY DIFFRACTION99.6600679864
3.9641-4.07120.2096033230782290.1765025118244745X-RAY DIFFRACTION99.5198079232
4.0712-4.1910.2136230431652290.1667559946154778X-RAY DIFFRACTION99.780789159
4.191-4.32620.1987932456182550.1624418180134732X-RAY DIFFRACTION99.74
4.3262-4.48070.1931037525772400.1544284470474750X-RAY DIFFRACTION99.6405750799
4.4807-4.660.1989527062892370.1477330101824750X-RAY DIFFRACTION99.8398398398
4.66-4.87190.1792455109232650.138725583794748X-RAY DIFFRACTION99.7611940299
4.8719-5.12860.1823879424682350.1390185083734724X-RAY DIFFRACTION99.9395405079
5.1286-5.44950.1776216804132520.1510611946154753X-RAY DIFFRACTION99.6218152866
5.4495-5.86970.2199725992622330.1601206120974784X-RAY DIFFRACTION99.8407960199
5.8697-6.45940.2080528249552410.1629311409894773X-RAY DIFFRACTION100
6.4594-7.39170.1970196634152300.1461228173174795X-RAY DIFFRACTION99.8013902681
7.3917-9.30360.1345324367882510.1128440598954797X-RAY DIFFRACTION99.7825657245
9.3036-51.10140.1958196949512580.1628614522284821X-RAY DIFFRACTION99.5687120173

+
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

-
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

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