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- PDB-5ts0: 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: 5ts0
タイトルStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2208
要素
  • Proteasome subunit alpha
  • Proteasome subunit beta
キーワードHYDRONLASE/HYDROLASE inhibitor / N / C-capped dipeptides / Mycobacterium tuberculosis / proteasome / inhibitors / HYDRONLASE-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 / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-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
(2S)-N-{(2S)-3-methoxy-1-[(naphthalen-1-ylmethyl)amino]-1-oxopropan-2-yl}-4-oxo-2-[(3-phenylpropanoyl)amino]-4-(1H-pyrrol-1-yl)butanamide (non-preferred name) / Chem-7J1 / 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: 2.84679745871 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9月27日Group: Author supporting evidence / Refinement description / カテゴリ: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
改定 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42024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

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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)725,21242
ポリマ－717,44728
非ポリマー7,76514
水6,269348
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 area84780 Å2
ΔGint-85 kcal/mol
Surface area220690 Å2
手法PISA
単位格子
Length a, b, c (Å)120.553, 198.542, 165.725
Angle α, β, γ (deg.)90.000, 103.243, 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 N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 7
121(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N8
131(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
141(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
151(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
161(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
171(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
181(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
191(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
211(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 7
221(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H8
231(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
241(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
251(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
261(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
271(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
281(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
291(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
311(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 7
321(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I8
331(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
341(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
351(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
361(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
371(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
381(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
391(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
411(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 7
421(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J8
431(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
441(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
451(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
461(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
471(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
481(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
491(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
511(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 7
521(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K8
531(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
541(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
551(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
561(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
571(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
581(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
591(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
611(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 7
621(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L8
631(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
641(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
651(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
661(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
671(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
681(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
691(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
711(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 7
721(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M8
731(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
741(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
751(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
761(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
771(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
781(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
791(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
811(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 7
821(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V8
831(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
841(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
851(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
861(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
871(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
881(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
891(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
911(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 7
921(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W8
931(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
941(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
951(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
961(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
971(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
981(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
991(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
1011(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 7
1021(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X8
1031(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1041(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1051(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1061(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1071(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1081(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1091(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1111(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 7
1121(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y8
1131(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1141(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1151(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1161(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1171(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1181(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1191(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1211(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 7
1221(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z8
1231(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1241(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1251(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1261(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1271(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1281(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1291(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1311(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A1 - 7
1321(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A8
1331(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1341(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1351(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1361(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1371(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1381(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1391(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1411(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B1 - 7
1421(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B8
1431(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1441(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1451(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1461(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1471(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1481(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1491(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
112(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9
122(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A12 - 13
132(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A15 - 21
142(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A23 - 25
152(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A27
162(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A29 - 34
172(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A35
182(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
192(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1102(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1112(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1122(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1132(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
1142(CHAIN A AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...A9 - 235
212(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9
222(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B12 - 13
232(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B15 - 21
242(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B23 - 25
252(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B27
262(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B29 - 34
272(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B35
282(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
292(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
2102(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
2112(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
2122(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
2132(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
2142(CHAIN B AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...B9 - 236
312(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9
322(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C12 - 13
332(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C15 - 21
342(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C23 - 25
352(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C27
362(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C29 - 34
372(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C35
382(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
392(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
3102(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
3112(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
3122(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
3132(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
3142(CHAIN C AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...C9 - 236
412(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9
422(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D12 - 13
432(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D15 - 21
442(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D23 - 25
452(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D27
462(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D29 - 34
472(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D35
482(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
492(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4102(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4112(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4122(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4132(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
4142(CHAIN D AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...D9 - 235
512(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9
522(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E12 - 13
532(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E15 - 21
542(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E23 - 25
552(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E27
562(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E29 - 34
572(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E35
582(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
592(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5102(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5112(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5122(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5132(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
5142(CHAIN E AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...E9 - 235
612(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9
622(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F12 - 13
632(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F15 - 21
642(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F23 - 25
652(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F27
662(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F29 - 34
672(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F35
682(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
692(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
6102(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
6112(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
6122(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
6132(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
6142(CHAIN F AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...F9 - 234
712(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9
722(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G12 - 13
732(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G15 - 21
742(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G23 - 25
752(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G27
762(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G29 - 34
772(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G35
782(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
792(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
7102(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
7112(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
7122(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
7132(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
7142(CHAIN G AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...G9 - 236
812(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9
822(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O12 - 13
832(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O15 - 21
842(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O23 - 25
852(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O27
862(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O29 - 34
872(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O35
882(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
892(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8102(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8112(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8122(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8132(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
8142(CHAIN O AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...O9 - 235
912(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9
922(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P12 - 13
932(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P15 - 21
942(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P23 - 25
952(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P27
962(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P29 - 34
972(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P35
982(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
992(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9102(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9112(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9122(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9132(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
9142(CHAIN P AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...P9 - 235
1012(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9
1022(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q12 - 13
1032(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q15 - 21
1042(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q23 - 25
1052(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q27
1062(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q29 - 34
1072(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q35
1082(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
1092(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10102(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10112(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10122(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10132(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
10142(CHAIN Q AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...Q9 - 236
1112(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9
1122(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R12 - 13
1132(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R15 - 21
1142(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R23 - 25
1152(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R27
1162(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R29 - 34
1172(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R35
1182(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
1192(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11102(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11112(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11122(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11132(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
11142(CHAIN R AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...R9 - 235
1212(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9
1222(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S12 - 13
1232(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S15 - 21
1242(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S23 - 25
1252(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S27
1262(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S29 - 34
1272(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S35
1282(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
1292(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12102(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12112(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12122(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12132(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
12142(CHAIN S AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...S9 - 236
1312(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9
1322(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T12 - 13
1332(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T15 - 21
1342(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T23 - 25
1352(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T27
1362(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T29 - 34
1372(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T35
1382(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
1392(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
13102(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
13112(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
13122(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
13132(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
13142(CHAIN T AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...T9 - 236
1412(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9
1422(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U12 - 13
1432(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U15 - 21
1442(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U23 - 25
1452(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U27
1462(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U29 - 34
1472(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U35
1482(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
1492(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14102(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14112(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14122(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14132(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235
14142(CHAIN U AND (RESSEQ 9 OR RESSEQ 12:13 OR RESSEQ...U9 - 235

NCSアンサンブル:
ID
1
2

-
要素

#1: タンパク質
Proteasome subunit alpha / 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 / 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-7J1 / (2S)-N-{(2S)-3-methoxy-1-[(naphthalen-1-ylmethyl)amino]-1-oxopropan-2-yl}-4-oxo-2-[(3-phenylpropanoyl)amino]-4-(1H-pyrrol-1-yl)butanamide (non-preferred name)


タイプ: Non-polymer / クラス: 阻害剤 / 分子量: 554.636 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C32H34N4O5
参照: (2S)-N-{(2S)-3-methoxy-1-[(naphthalen-1-ylmethyl)amino]-1-oxopropan-2-yl}-4-oxo-2-[(3-phenylpropanoyl)amino]-4-(1H-pyrrol-1-yl)butanamide (non-preferred name)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 348 / 由来タイプ: 天然 / 式: H2O

-
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: 2.69 Å3/Da / 溶媒含有率: 54.29 %
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) and 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8月24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: 2.85→50 Å / Num. obs: 171593 / % possible obs: 98.2 % / 冗長度: 3.5 % / Biso Wilson estimate: 52.0500839445 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.3
反射 シェル解像度: 2.85→2.95 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.701 / % possible all: 95.4

-
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 / 解像度: 2.84679745871→49.6146034077 Å / SU ML: 0.36721423524 / 交差検証法: FREE R-VALUE / σ(F): 1.33540022557 / 位相誤差: 24.1868010231
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.235101775159 8304 4.84034553912 %
Rwork0.176839579492 163254 -
obs0.179644519197 171558 96.8652250014 %
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: 52.9637247037 Å2
精密化ステップサイクル: LAST / 解像度: 2.84679745871→49.6146034077 Å
タンパク質核酸リガンド溶媒全体
原子数46389 0 574 348 47311
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01026246726147677
X-RAY DIFFRACTIONf_angle_d1.2132392579564491
X-RAY DIFFRACTIONf_chiral_restr0.06739018018617289
X-RAY DIFFRACTIONf_plane_restr0.00835115068538475
X-RAY DIFFRACTIONf_dihedral_angle_d18.104301328428469
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8468-2.87910.3375543638652150.2647300784794400X-RAY DIFFRACTION78.3398404346
2.8791-2.9130.3403740440982410.258977824974868X-RAY DIFFRACTION86.8286879674
2.913-2.94850.3509587730012480.2484666588235045X-RAY DIFFRACTION89.6359017782
2.9485-2.98590.3203380635732790.2289168751115089X-RAY DIFFRACTION91.7606837607
2.9859-3.02510.2948530090012510.2241733857165321X-RAY DIFFRACTION94.6331521739
3.0251-3.06660.2981313373652810.2162285914495367X-RAY DIFFRACTION96.1689085646
3.0666-3.11040.2945728182082730.2283432376865446X-RAY DIFFRACTION97.1627590894
3.1104-3.15680.3229844610522660.2306451349555464X-RAY DIFFRACTION97.3827328348
3.1568-3.20610.3075452461272760.2248788526825481X-RAY DIFFRACTION97.6424694708
3.2061-3.25870.2843778896972730.208790553515539X-RAY DIFFRACTION97.9770734997
3.2587-3.31480.2748225245472870.2053416919025485X-RAY DIFFRACTION98.1132075472
3.3148-3.37510.2692560460313000.1997271673165441X-RAY DIFFRACTION98.187104498
3.3751-3.440.2519251483452840.1950959752785564X-RAY DIFFRACTION98.5009263938
3.44-3.51020.2437289286442970.1913949708745484X-RAY DIFFRACTION98.5005963537
3.5102-3.58650.2746678114952880.1876884841245535X-RAY DIFFRACTION98.594649509
3.5865-3.66990.2558060244692920.1977427436445525X-RAY DIFFRACTION98.6768447837
3.6699-3.76170.2613009963992590.1846814306895567X-RAY DIFFRACTION98.7457627119
3.7617-3.86330.2497475276953000.1796791462485525X-RAY DIFFRACTION98.879646919
3.8633-3.9770.2286040295762800.1705592454695528X-RAY DIFFRACTION98.7923116176
3.977-4.10530.2253825802592830.1677055642455561X-RAY DIFFRACTION98.966977138
4.1053-4.25190.2061155058022940.1669201479885543X-RAY DIFFRACTION98.9657511021
4.2519-4.42210.209087537572940.1567593008955538X-RAY DIFFRACTION99.0489130435
4.4221-4.62320.1733274092942970.1503396078225599X-RAY DIFFRACTION99.1924629879
4.6232-4.86670.1944915380562470.1448058388165577X-RAY DIFFRACTION99.0981793432
4.8667-5.17130.2195055627752680.1498887316355642X-RAY DIFFRACTION99.2943548387
5.1713-5.57010.1987557346032750.1542722585895581X-RAY DIFFRACTION99.3384223919
5.5701-6.12980.2401083237292810.1701223417645609X-RAY DIFFRACTION99.3422162253
6.1298-7.01460.221196789153100.1612451351515592X-RAY DIFFRACTION99.5278246206
7.0146-8.82960.1628999675522920.1245268403845644X-RAY DIFFRACTION99.4638069705
8.8296-49.62210.1855493248442730.1576339190565694X-RAY DIFFRACTION99.0537848606

+
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

-
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

+
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

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