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- PDB-6ult: BRD2-BD2 in complex with the cyclic peptide 4.2_3 -

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基本情報

登録情報
データベース: PDB / ID: 6ult
タイトルBRD2-BD2 in complex with the cyclic peptide 4.2_3
要素
  • Bromodomain-containing protein 2
  • Cyclic peptide 4.2_3
キーワードTRANSCRIPTION/INHIBITOR / BET / bromodomain / macrocyclic peptide / BRD2 / inhibitor / RaPID / TRANSCRIPTION-INHIBITOR complex / TRANSCRIPTION
機能・相同性
機能・相同性情報


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
類似検索 - 分子機能
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
類似検索 - ドメイン・相同性
Bromodomain-containing protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Patel, K. / Walshe, J.L. / Walport, L.J. / Mackay, J.P.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)APP1161623 オーストラリア
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: Cyclic peptides can engage a single binding pocket through highly divergent modes.
著者: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, ...著者: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Mackay, J.P.
履歴
登録2019年10月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年2月24日Provider: repository / タイプ: Initial release
改定 1.12021年3月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月11日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.32023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
改定 1.42024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
E: Bromodomain-containing protein 2
F: Bromodomain-containing protein 2
G: Bromodomain-containing protein 2
H: Bromodomain-containing protein 2
I: Cyclic peptide 4.2_3
J: Cyclic peptide 4.2_3
K: Cyclic peptide 4.2_3
L: Cyclic peptide 4.2_3


分子量 (理論値)分子数
合計 (水以外)109,34212
ポリマ－109,34212
非ポリマー00
水1,44180
1
A: Bromodomain-containing protein 2
K: Cyclic peptide 4.2_3

C: Bromodomain-containing protein 2


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: surface plasmon resonance
  • 27.3 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)27,3363
ポリマ－27,3363
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area12520 Å2
手法PISA
2
B: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2

L: Cyclic peptide 4.2_3


  • 登録者・ソフトウェアが定義した集合体
  • 27.3 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)27,3363
ポリマ－27,3363
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area13030 Å2
手法PISA
3
E: Bromodomain-containing protein 2
J: Cyclic peptide 4.2_3

G: Bromodomain-containing protein 2


  • 登録者・ソフトウェアが定義した集合体
  • 27.3 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)27,3363
ポリマ－27,3363
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2790 Å2
ΔGint-21 kcal/mol
Surface area12660 Å2
手法PISA
4
H: Bromodomain-containing protein 2
I: Cyclic peptide 4.2_3

F: Bromodomain-containing protein 2


  • 登録者・ソフトウェアが定義した集合体
  • 27.3 kDa, 3 ポリマー
分子量 (理論値)分子数
合計 (水以外)27,3363
ポリマ－27,3363
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area12640 Å2
手法PISA
単位格子
Length a, b, c (Å)77.083, 63.627, 120.339
Angle α, β, γ (deg.)90.000, 108.388, 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
12
22
13
23

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSLEULEU(chain 'A' and (resid 353 through 357 or resid 359...AA353 - 3578 - 12
121GLUGLUSERSER(chain 'A' and (resid 353 through 357 or resid 359...AA359 - 36214 - 17
131HISHISTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA365 - 37320 - 28
141PROPROASPASP(chain 'A' and (resid 353 through 357 or resid 359...AA375 - 37730 - 32
151GLYGLYLEULEU(chain 'A' and (resid 353 through 357 or resid 359...AA382 - 38337 - 38
161ASPASPILEILE(chain 'A' and (resid 353 through 357 or resid 359...AA385 - 39040 - 45
171HISHISVALVAL(chain 'A' and (resid 353 through 357 or resid 359...AA392 - 39947 - 54
181LYSLYSASNASN(chain 'A' and (resid 353 through 357 or resid 359...AA402 - 40557 - 60
191TYRTYRTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA40863
1101ASPASPASPASP(chain 'A' and (resid 353 through 357 or resid 359...AA41065
1111GLUGLUVALVAL(chain 'A' and (resid 353 through 357 or resid 359...AA413 - 41868 - 73
1121LEULEUMETMET(chain 'A' and (resid 353 through 357 or resid 359...AA420 - 43875 - 93
1131LYSLYSGLUGLU(chain 'A' and (resid 353 through 357 or resid 359...AA441 - 44796 - 102
1141TYRTYRTYRTYR(chain 'A' and (resid 353 through 357 or resid 359...AA450105
211CYSCYSLEULEU(chain 'B' and (resid 353 through 357 or resid 359...BB353 - 3578 - 12
221GLUGLUSERSER(chain 'B' and (resid 353 through 357 or resid 359...BB359 - 36214 - 17
231HISHISTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB365 - 37320 - 28
241PROPROASPASP(chain 'B' and (resid 353 through 357 or resid 359...BB375 - 37730 - 32
251GLYGLYLEULEU(chain 'B' and (resid 353 through 357 or resid 359...BB382 - 38337 - 38
261ASPASPILEILE(chain 'B' and (resid 353 through 357 or resid 359...BB385 - 39040 - 45
271HISHISVALVAL(chain 'B' and (resid 353 through 357 or resid 359...BB392 - 39947 - 54
281LYSLYSASNASN(chain 'B' and (resid 353 through 357 or resid 359...BB402 - 40557 - 60
291TYRTYRTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB40863
2101ASPASPASPASP(chain 'B' and (resid 353 through 357 or resid 359...BB41065
2111GLUGLUVALVAL(chain 'B' and (resid 353 through 357 or resid 359...BB413 - 41868 - 73
2121LEULEUMETMET(chain 'B' and (resid 353 through 357 or resid 359...BB420 - 43875 - 93
2131LYSLYSGLUGLU(chain 'B' and (resid 353 through 357 or resid 359...BB441 - 44796 - 102
2141TYRTYRTYRTYR(chain 'B' and (resid 353 through 357 or resid 359...BB450105
311CYSCYSLEULEU(chain 'C' and (resid 353 through 357 or resid 359...CC353 - 3578 - 12
321GLUGLUSERSER(chain 'C' and (resid 353 through 357 or resid 359...CC359 - 36214 - 17
331HISHISTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC365 - 37320 - 28
341PROPROASPASP(chain 'C' and (resid 353 through 357 or resid 359...CC375 - 37730 - 32
351GLYGLYLEULEU(chain 'C' and (resid 353 through 357 or resid 359...CC382 - 38337 - 38
361ASPASPILEILE(chain 'C' and (resid 353 through 357 or resid 359...CC385 - 39040 - 45
371HISHISVALVAL(chain 'C' and (resid 353 through 357 or resid 359...CC392 - 39947 - 54
381LYSLYSASNASN(chain 'C' and (resid 353 through 357 or resid 359...CC402 - 40557 - 60
391TYRTYRTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC40863
3101ASPASPASPASP(chain 'C' and (resid 353 through 357 or resid 359...CC41065
3111GLUGLUVALVAL(chain 'C' and (resid 353 through 357 or resid 359...CC413 - 41868 - 73
3121LEULEUMETMET(chain 'C' and (resid 353 through 357 or resid 359...CC420 - 43875 - 93
3131LYSLYSGLUGLU(chain 'C' and (resid 353 through 357 or resid 359...CC441 - 44796 - 102
3141TYRTYRTYRTYR(chain 'C' and (resid 353 through 357 or resid 359...CC450105
411CYSCYSLEULEU(chain 'D' and (resid 353 through 357 or resid 359...DD353 - 3578 - 12
421GLUGLUSERSER(chain 'D' and (resid 353 through 357 or resid 359...DD359 - 36214 - 17
431HISHISTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD365 - 37320 - 28
441PROPROASPASP(chain 'D' and (resid 353 through 357 or resid 359...DD375 - 37730 - 32
451GLYGLYLEULEU(chain 'D' and (resid 353 through 357 or resid 359...DD382 - 38337 - 38
461ASPASPILEILE(chain 'D' and (resid 353 through 357 or resid 359...DD385 - 39040 - 45
471HISHISVALVAL(chain 'D' and (resid 353 through 357 or resid 359...DD392 - 39947 - 54
481LYSLYSASNASN(chain 'D' and (resid 353 through 357 or resid 359...DD402 - 40557 - 60
491TYRTYRTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD40863
4101ASPASPASPASP(chain 'D' and (resid 353 through 357 or resid 359...DD41065
4111GLUGLUVALVAL(chain 'D' and (resid 353 through 357 or resid 359...DD413 - 41868 - 73
4121LEULEUMETMET(chain 'D' and (resid 353 through 357 or resid 359...DD420 - 43875 - 93
4131LYSLYSGLUGLU(chain 'D' and (resid 353 through 357 or resid 359...DD441 - 44796 - 102
4141TYRTYRTYRTYR(chain 'D' and (resid 353 through 357 or resid 359...DD450105
511CYSCYSLEULEU(chain 'E' and (resid 353 through 357 or resid 359...EE353 - 3578 - 12
521GLUGLUSERSER(chain 'E' and (resid 353 through 357 or resid 359...EE359 - 36214 - 17
531HISHISTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE365 - 37320 - 28
541PROPROASPASP(chain 'E' and (resid 353 through 357 or resid 359...EE375 - 37730 - 32
551GLYGLYLEULEU(chain 'E' and (resid 353 through 357 or resid 359...EE382 - 38337 - 38
561ASPASPILEILE(chain 'E' and (resid 353 through 357 or resid 359...EE385 - 39040 - 45
571HISHISVALVAL(chain 'E' and (resid 353 through 357 or resid 359...EE392 - 39947 - 54
581LYSLYSASNASN(chain 'E' and (resid 353 through 357 or resid 359...EE402 - 40557 - 60
591TYRTYRTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE40863
5101ASPASPASPASP(chain 'E' and (resid 353 through 357 or resid 359...EE41065
5111GLUGLUVALVAL(chain 'E' and (resid 353 through 357 or resid 359...EE413 - 41868 - 73
5121LEULEUMETMET(chain 'E' and (resid 353 through 357 or resid 359...EE420 - 43875 - 93
5131LYSLYSGLUGLU(chain 'E' and (resid 353 through 357 or resid 359...EE441 - 44796 - 102
5141TYRTYRTYRTYR(chain 'E' and (resid 353 through 357 or resid 359...EE450105
611CYSCYSLEULEU(chain 'F' and (resid 353 through 357 or resid 359...FF353 - 3578 - 12
621GLUGLUSERSER(chain 'F' and (resid 353 through 357 or resid 359...FF359 - 36214 - 17
631HISHISTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF365 - 37320 - 28
641PROPROASPASP(chain 'F' and (resid 353 through 357 or resid 359...FF375 - 37730 - 32
651GLYGLYLEULEU(chain 'F' and (resid 353 through 357 or resid 359...FF382 - 38337 - 38
661ASPASPILEILE(chain 'F' and (resid 353 through 357 or resid 359...FF385 - 39040 - 45
671HISHISVALVAL(chain 'F' and (resid 353 through 357 or resid 359...FF392 - 39947 - 54
681LYSLYSASNASN(chain 'F' and (resid 353 through 357 or resid 359...FF402 - 40557 - 60
691TYRTYRTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF40863
6101ASPASPASPASP(chain 'F' and (resid 353 through 357 or resid 359...FF41065
6111GLUGLUVALVAL(chain 'F' and (resid 353 through 357 or resid 359...FF413 - 41868 - 73
6121LEULEUMETMET(chain 'F' and (resid 353 through 357 or resid 359...FF420 - 43875 - 93
6131LYSLYSGLUGLU(chain 'F' and (resid 353 through 357 or resid 359...FF441 - 44796 - 102
6141TYRTYRTYRTYR(chain 'F' and (resid 353 through 357 or resid 359...FF450105
711CYSCYSLEULEU(chain 'G' and (resid 353 through 357 or resid 359...GG353 - 3578 - 12
721GLUGLUSERSER(chain 'G' and (resid 353 through 357 or resid 359...GG359 - 36214 - 17
731HISHISTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG365 - 37320 - 28
741PROPROASPASP(chain 'G' and (resid 353 through 357 or resid 359...GG375 - 37730 - 32
751GLYGLYLEULEU(chain 'G' and (resid 353 through 357 or resid 359...GG382 - 38337 - 38
761ASPASPILEILE(chain 'G' and (resid 353 through 357 or resid 359...GG385 - 39040 - 45
771HISHISVALVAL(chain 'G' and (resid 353 through 357 or resid 359...GG392 - 39947 - 54
781LYSLYSASNASN(chain 'G' and (resid 353 through 357 or resid 359...GG402 - 40557 - 60
791TYRTYRTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG40863
7101ASPASPASPASP(chain 'G' and (resid 353 through 357 or resid 359...GG41065
7111GLUGLUVALVAL(chain 'G' and (resid 353 through 357 or resid 359...GG413 - 41868 - 73
7121LEULEUMETMET(chain 'G' and (resid 353 through 357 or resid 359...GG420 - 43875 - 93
7131LYSLYSGLUGLU(chain 'G' and (resid 353 through 357 or resid 359...GG441 - 44796 - 102
7141TYRTYRTYRTYR(chain 'G' and (resid 353 through 357 or resid 359...GG450105
811CYSCYSLEULEU(chain 'H' and (resid 353 through 357 or resid 359...HH353 - 3578 - 12
821GLUGLUSERSER(chain 'H' and (resid 353 through 357 or resid 359...HH359 - 36214 - 17
831HISHISTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH365 - 37320 - 28
841PROPROASPASP(chain 'H' and (resid 353 through 357 or resid 359...HH375 - 37730 - 32
851GLYGLYLEULEU(chain 'H' and (resid 353 through 357 or resid 359...HH382 - 38337 - 38
861ASPASPILEILE(chain 'H' and (resid 353 through 357 or resid 359...HH385 - 39040 - 45
871HISHISVALVAL(chain 'H' and (resid 353 through 357 or resid 359...HH392 - 39947 - 54
881LYSLYSASNASN(chain 'H' and (resid 353 through 357 or resid 359...HH402 - 40557 - 60
891TYRTYRTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH40863
8101ASPASPASPASP(chain 'H' and (resid 353 through 357 or resid 359...HH41065
8111GLUGLUVALVAL(chain 'H' and (resid 353 through 357 or resid 359...HH413 - 41868 - 73
8121LEULEUMETMET(chain 'H' and (resid 353 through 357 or resid 359...HH420 - 43875 - 93
8131LYSLYSGLUGLU(chain 'H' and (resid 353 through 357 or resid 359...HH441 - 44796 - 102
8141TYRTYRTYRTYR(chain 'H' and (resid 353 through 357 or resid 359...HH450105
112TRPTRPILEILE(chain 'I' and resid 0 through 11)II1 - 112 - 12
212TRPTRPILEILEchain 'K'KK1 - 112 - 12
113TRPTRPALYALY(chain 'J' and resid 0 through 9)JJ1 - 92 - 10
213TRPTRPALYALYchain 'L'LL1 - 92 - 10

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


分子量: 12829.737 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BRD2, KIAA9001, RING3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P25440
#2: タンパク質・ペプチド
Cyclic peptide 4.2_3


分子量: 1676.039 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 80 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.48 Å3/Da / 溶媒含有率: 50.32 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX1 / 波長: 0.953724980354 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2018年11月8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: 0.953724980354 Å / 相対比: 1
反射解像度: 2.797→48.01 Å / Num. obs: 27310 / % possible obs: 98.8 % / 冗長度: 3.7 % / Biso Wilson estimate: 38.57 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.4
反射 シェル解像度: 2.8→2.95 Å / Num. unique obs: 3757 / CC1/2: 0.77

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PHENIX1.14_3260精密化
XDSデータ削減
Aimless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: 3ONI

3oni


解像度: 2.8→42.5 Å / SU ML: 0.4947 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 37.5455 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.3353 1384 5.09 %
Rwork0.2844 25812 -
obs0.287 27196 98.23 %
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: 57.39 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→42.5 Å
タンパク質核酸リガンド溶媒全体
原子数7427 0 0 80 7507
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00287652
X-RAY DIFFRACTIONf_angle_d0.65410287
X-RAY DIFFRACTIONf_chiral_restr0.03841034
X-RAY DIFFRACTIONf_plane_restr0.00351319
X-RAY DIFFRACTIONf_dihedral_angle_d13.77544653
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.41891320.34542368X-RAY DIFFRACTION90.91
2.9-3.010.37731480.33342568X-RAY DIFFRACTION99.2
3.01-3.150.41471140.3382586X-RAY DIFFRACTION99.23
3.15-3.320.36541650.29352593X-RAY DIFFRACTION99.39
3.32-3.520.30031240.28022593X-RAY DIFFRACTION99.09
3.52-3.80.31391280.27662618X-RAY DIFFRACTION99.31
3.8-4.180.3461470.26322586X-RAY DIFFRACTION99.06
4.18-4.780.31891250.25522616X-RAY DIFFRACTION98.99
4.78-6.020.32771550.28272621X-RAY DIFFRACTION99.21
6.02-42.50.28431460.27182663X-RAY DIFFRACTION97.94
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4399272108161.10069363776-0.7369663106493.59609425995-2.879431598022.941976528550.175936781522-0.4032981760630.00945652579830.514985148827-0.4028425314170.209533585834-0.00500057657910.195238620730.2049912589070.4242108144440.1007078343060.07244923993721.49427702459-0.08917777333670.3553971994934.640203634976.1667084715460.4703208686
27.10635031352-5.7989632507-0.5723686000377.498614830991.474317047818.98007510010.6905267378780.8927731635470.736226788131-1.0005743477-0.546116071065-0.745913638789-0.04595402324350.766335673827-0.1611680962050.3347423301230.01065573146880.06402481814220.5318169005850.01857214385690.4216605362377.367425781343.314468694741.0764742584
36.1093620805-0.7523641103260.4643541266918.63539321927-1.138584031518.7348031269-0.161249768622-0.463141586837-1.298003956660.4813914432860.1505233910181.235840438690.55913342876-1.886406007450.0273665370810.409445948677-0.101473695090.06058171737320.9195573325520.127483730830.5514219207134.59199029568-7.5846108392156.900452476
42.877383456492.19282654067-1.510813648435.24692381664-1.039604150574.204728115380.0789903950331-1.228362958-0.1306086059950.388985750307-0.340122601236-0.111184329070.03426151926380.8271532346280.2679374978230.2960834424730.02526744795030.09270256433281.005787200040.0211492442210.41508100683714.23865095295.7779274250954.995076471
55.31773624186-1.34851243615-1.518930281052.00197152659-8.153306014057.66651416019-0.0491665373962-0.583848427190.08434686927731.148363479020.6918900921510.0451203485368-0.945270611875-0.602262670588-0.6307664158240.5717317707360.080438592850.02366770455410.967507375519-0.2475955757450.43718882099384.3555733664-33.467120608967.513517856
60.02963492732420.06711928198130.1623402107381.09428692048-0.09593904276051.28374837920.1724978929710.0320396318526-0.0127390414824-0.00855612426572-0.02142206752630.1711809645860.541053810031-0.542203667446-0.1854166114160.5697192282950.0147463887731-0.1302697300351.39914964973-0.1030280484240.34227347584882.5815810736-31.749691143150.6996264317
70.5877880671630.805192715159-0.2532505861532.51381392171-1.344318045366.45783006386-0.03905906816570.622809576552-0.0171332866808-0.564725941304-0.1517266060110.03105824844810.8896789088310.1382567419570.2003668309750.4796044391920.0648608603941-0.02280900782461.33565704837-0.1968780243450.29418642720991.2878122111-32.025813616752.985217395
80.4085059001230.4744891182030.01639927833882.05233849797-0.7749579533554.177089378930.07283837513130.6352629958890.106795318517-0.231382113864-0.2297621096540.2027396884290.03271231891810.09693784011790.1376834620760.337856509719-0.0295270131817-0.01695505082411.36422160922-0.0753043307780.43152545228391.2010655476-22.548521484256.1018305929
91.912068787872.92916548941.321522316676.385947977-0.5879701373834.49660291071-0.05033908764840.1385083814670.413391289171-0.005288536640420.361056920170.05345947714550.269796777233-0.614035390406-0.3241511992620.4673257527590.237192121070.07110033315221.11111765828-0.04484307190210.6029688535652.429733154610.730676670633.2155406456
101.25704873926-1.8162163951-2.201010219444.755413300181.544749132285.10778017698-0.5228891480480.459757375954-0.2542549608520.241151941010.659243715423-0.5876128557460.5148141492081.21555161257-0.09534661320660.2823243228850.03578812432290.1067079199450.6848171474310.02940653809450.57333714731667.72616600139.0637000312946.2969153192
112.005234317794.060811350355.354347421786.440627308322.108019269034.159526521780.114357686896-0.7762078084610.01087197504790.849923258349-0.1556046689660.8541553447160.494292245252-1.147601713320.06827087019210.383890983386-0.04755354611050.1307160984440.879314335899-0.09535645018730.48537560660256.260515032312.780394631347.9347086309
122.110033228210.766257480638-2.086521274251.09437712395-0.2494088164862.378769175370.09004627544250.4339475539740.1653748737040.129260891199-0.1913267069850.6736737145210.278568411094-0.2765025849130.1204209202270.6414620544020.1757522878750.2502542864251.567394252-0.1367489193070.78939100163141.56743285713.496934875447.8361984693
135.509013502413.082518152594.801291728283.732406582550.5348057811226.49768892753-0.0214868479149-0.6938473602040.709350113502-0.08984003713090.1415095910340.411392536595-0.806115231462-0.678960044415-0.1104805241160.4857898522380.1471157027560.06310650835830.459317778477-0.04381545735560.22999848816155.547440563220.077647028343.0196541614
149.778866766331.03499833177-0.1304263640381.223273525911.654601485842.75293292277-0.2908247004490.7973815685590.3814740885-0.4327661620920.289003013119-0.0233626984945-0.392660519311-0.3839042841450.007460747797480.416722129261-0.0868622124350.04770174102620.867567078150.1264378161610.37171180087659.206720835520.059092356833.6763730142
152.000496570283.56022907311-5.677559349632.467243217610.3739624457369.581492113510.1480457203660.2686471178050.3111298555340.2519336416540.2183247004971.81833817612-0.547192706334-1.09374081251-0.3442211002390.510610712251-0.1029811058610.1898561338731.154168193220.19965530241.0355542323742.2724611577-21.31781336336.037613634
161.56197281173-1.001671863752.530790012561.85070042692-1.057257256664.35442205152-0.1620698094070.08122007603220.1103039332520.0153203453415-0.318024617864-0.193035434068-0.1460469615380.38468150270.4584879383120.421735993058-0.00854986599902-0.08998552840421.48726194256-0.07110856616710.38765146520862.4880956232-25.643932861138.8802005245
175.763032394130.4941113887250.7665490726120.884647325894-0.7342502002452.769543776580.0336858034287-0.335041340330.1643206003640.07332606266830.2733594230730.0465457427284-0.1039170217820.00598681239978-0.2743552058880.491661005775-0.03797831004690.03663374587352.02515105989-0.05382706914420.47089476028362.0467978543-17.403995464849.9277292158
180.732779075192-0.195429590335-0.5688319828221.657105537920.7041148987691.336071407630.0546474005633-0.1145927010270.04002812232180.340839731593-0.2065122073950.3402261808830.0123703926224-0.2912260988190.1004800941250.4581543239610.06775914012330.07646665218871.86892306599-0.01902468158010.33743591095450.8054525729-18.675845312644.1813524404
194.79131908589-2.845219313042.99856586558.594023981623.434112606775.815000496540.201492701080.4084724620620.594948276053-1.49682166138-0.355480498401-2.21508840589-0.2874108496731.007258512580.1451890723930.471269482291-0.1426660191840.3239050953481.209390711120.03239202437520.69448424255770.6751378017-14.17125064436.3417765826
202.956253012720.63483770947-1.094958074070.133618210193-0.232150352330.406550006930.2855955415680.6400452518830.339062532031-0.160365991657-0.008234760621910.245650537796-0.315476074682-0.653731556492-0.2581423081290.5937115136480.1621715904920.1270388393241.64629706838-0.0117337086130.40515789908754.1496287425-15.003298295631.9109246704
217.006136943131.66917231755-0.007795802213185.01598998476-1.140483381783.25911207213-0.243758058449-0.0398976483533-0.124108500215-0.6417992175280.145593122634-0.3225805858320.2660899310070.04697119408720.08344434833750.235384018030.01603865665350.110718052824-0.01338804780860.1201663328310.37569848091752.588492103616.3807417069-4.70290521485
224.63438360271-0.106087906754-0.335132897012.161631302620.838746736442.71640060545-0.114894350178-1.356761531-0.3181444793210.33869704469-0.1224608812230.03820052970780.2303962237650.09431294785750.1927608352430.1554686306360.05119229132550.05110865410320.4498914377620.08361190589780.35137233481448.779584388413.03309124648.43822999492
232.671621038151.143359335372.076101342626.204751741111.440628009924.555591285890.1530853778120.05414226306860.112833174277-0.243289476614-0.121418791609-0.0861173848887-0.2320812697560.138629563951-0.07910101553340.08840322087090.1134145342210.09107648928050.0335734525887-0.1661160505660.62265843438644.151677894820.5915528253-2.84342475353
242.318307213974.152771872841.198016976429.419858994185.311981567125.6917718333-0.1683046959640.577305695905-1.02018037847-0.307353128659-0.1676127331181.015304334030.805073761072-0.0434860515710.3640878205120.513239917190.1424066692980.1304726058060.368376925671-0.1137182799071.0668192668151.0983852626-20.7414944005-10.3804763214
252.67857320902-0.4228723725731.109608269893.140707608750.9389952650562.430212839420.161041832465-0.562888538865-0.3532542125780.4693825615260.00817842027523-0.006631539028980.308795304883-0.078451710352-0.1310998453870.264037869213-0.01280363516470.1164115134140.1320792981150.1841596133040.5221036685154.4886885677-11.80562260268.47493475249
261.548106932030.35447963739-0.8192004644723.459308123072.02255740585.947213358620.0206580741446-0.348897962743-0.3868120182670.0008832919853910.08938608528940.06445877910320.643271416739-0.0951862095981-0.03996819097530.262204711502-0.0667139839775-0.06474509747190.1275963727850.04849086633560.48233377771850.9601811141-22.50407261987.72166471308
271.42361230856-1.33256979976-0.6141857389963.246973472460.7645408875482.647207611050.19773491673-0.16828845218-0.292308491740.0962668095997-0.05714810969650.02849873584650.5149320526850.0105196671798-0.09626988742430.1865655490590.02650422113950.1040208446650.0398218018619-0.008808767172660.58807150636245.2414353178-19.62580636163.74216759981
280.8541064541771.011911586410.8258904277811.264214498610.7217965183481.595762176390.162442137480.419561824072-0.0824043906157-0.311050238139-0.1676254229960.03649862546390.006394064951390.02526086478450.0122842419645-0.04933147984210.5753693335420.1564208114080.035120532744-0.02790146778430.6755115376144.4410266873-10.6065257576-2.2221398221
290.526425767467-0.644419131853-0.6435470324991.71262050682-0.00203821831671.447610140730.5415492970170.466998346620.0216286977573-0.381955864026-0.01853561725960.1073295437270.2214381951220.946873693863-0.5371338566550.96707546021-0.172252832449-0.07464950859671.082799021180.1578433667240.4327909574984.3539618804123.937411058624.214797694
300.641882213299-0.582150106620.8792941947482.26083008289-0.0551361916171.51631323138-0.0001703753754160.281122017584-0.03029634219730.05125347616930.05671684832630.0480271774332-0.4619470825890.971953418655-0.05220645565380.272397243068-0.4336208729050.0638950558321.388431011490.06470236511270.488882060496-7.3024584636225.30472621528.86261484133
311.108579752470.584629472681-0.7704626516821.33338339485-1.303210762471.320283332770.000273524582447-0.0453220555991-0.0030718088347-0.2531066939740.120420240518-0.361451574379-0.002291973194360.464680552233-0.1004095390430.564928677485-0.325460293750.08771609226891.95338411457-0.1072862987810.6016687672418.605170458822.341896624712.2781806017
320.67441220390.248907567159-0.255039681690.864333156933-0.0245889622490.327080215754-0.00968086366928-0.154104934810.077815943011-0.1481678027380.118894729065-0.38400739844-0.05954645731270.516501655614-0.1092352146040.670587640514-0.370100648780.01041497809741.82348250667-0.0302688078320.4169742884372.8015101072332.43500705613.9428414711
332.387853771190.7320053834531.50141345612.925958664290.3366439506346.92682658581-0.2901783410850.1564763148870.2174729070820.358421948576-0.0119792095854-0.172164870122-0.3841906751280.2057372232740.2821610096020.861404066207-0.112659765631-0.08440795962791.1506835888-0.04728919109950.28632717814.1717187663833.750304168724.7127039404
344.99158096134-2.09686396818-0.3758442420012.619045908281.102941777740.5408832275490.377842255628-0.9754321616140.07336414951410.255180478326-0.575619120174-0.5003943521330.1173274706870.90719963290.1602539895610.428191383973-0.191365774545-0.03276943702781.112081768940.02122765663830.4152508785059.2698274207-11.35157781422.6257426527
353.220309970410.085796234333-1.022247735011.32780666418-0.5726893942021.047625157220.0989016096263-0.8981010814050.3791396776480.0876695372216-0.228897427071-0.09200570962160.2215801310820.2792219662330.03962553662960.270147471706-0.2279814466440.1480269823790.384901455833-0.1885473278830.5066813241961.63762277051-5.7128026030715.7921412514
364.516187325041.283172761740.5486969579191.67403927922-0.4272478585620.3272544965210.034136253897-0.8383637658090.7309688612270.599751410043-0.07093913201920.586474371872-0.124522201393-0.0271119919180.04040158940410.2754386127790.03275522847180.1022407604030.433037861234-0.1542142686840.386668431475-20.1150438128-5.8413966934916.3445557335
373.225588580881.676564109321.654177164863.423853843111.996453442213.06426223091-0.455986225473-0.01568401802130.2687479977470.2580054874280.009334766328360.2665306706260.2618531764030.1612578492480.4290608040130.5797337923250.135273377785-0.1244687312320.823118975781-0.2866255212820.49158306273957.909244219928.150482395314.5054855482
382.00023644417-5.669328407830.8761406420313.72963156407-1.57727704561.70876751724-0.4249197275660.2517912607360.496331728166-0.3010897225880.278956500493-0.723247239581-0.5064279453530.3077185470860.1384531945110.565110396969-0.1844019497830.1006152373620.600759601108-0.2409901445510.4508214008010.70232363399615.578408373142.517015941
393.19845575431-0.662633585793-2.537135557513.288537816472.870259287035.71493707634-0.00763043008736-0.281214167028-0.0637425502498-0.01888644564260.0644238853960.1328080302510.121749112139-0.198924661029-0.05498710835850.802327463728-0.03061710868950.003985350777951.0392331661-0.07575284838620.2260083558941.238083529413.410597904472.1229556531
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 351 through 372 )
2X-RAY DIFFRACTION2chain 'A' and (resid 373 through 395 )
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 410 )
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 454 )
5X-RAY DIFFRACTION5chain 'B' and (resid 346 through 360 )
6X-RAY DIFFRACTION6chain 'B' and (resid 361 through 410 )
7X-RAY DIFFRACTION7chain 'B' and (resid 411 through 428 )
8X-RAY DIFFRACTION8chain 'B' and (resid 429 through 453 )
9X-RAY DIFFRACTION9chain 'C' and (resid 351 through 372 )
10X-RAY DIFFRACTION10chain 'C' and (resid 373 through 385 )
11X-RAY DIFFRACTION11chain 'C' and (resid 386 through 404 )
12X-RAY DIFFRACTION12chain 'C' and (resid 405 through 410 )
13X-RAY DIFFRACTION13chain 'C' and (resid 411 through 428 )
14X-RAY DIFFRACTION14chain 'C' and (resid 429 through 451 )
15X-RAY DIFFRACTION15chain 'D' and (resid 347 through 360 )
16X-RAY DIFFRACTION16chain 'D' and (resid 361 through 385 )
17X-RAY DIFFRACTION17chain 'D' and (resid 386 through 395 )
18X-RAY DIFFRACTION18chain 'D' and (resid 396 through 428 )
19X-RAY DIFFRACTION19chain 'D' and (resid 429 through 433 )
20X-RAY DIFFRACTION20chain 'D' and (resid 434 through 453 )
21X-RAY DIFFRACTION21chain 'E' and (resid 346 through 372 )
22X-RAY DIFFRACTION22chain 'E' and (resid 373 through 433 )
23X-RAY DIFFRACTION23chain 'E' and (resid 434 through 454 )
24X-RAY DIFFRACTION24chain 'F' and (resid 346 through 360 )
25X-RAY DIFFRACTION25chain 'F' and (resid 361 through 385 )
26X-RAY DIFFRACTION26chain 'F' and (resid 386 through 404 )
27X-RAY DIFFRACTION27chain 'F' and (resid 405 through 433 )
28X-RAY DIFFRACTION28chain 'F' and (resid 434 through 453 )
29X-RAY DIFFRACTION29chain 'G' and (resid 353 through 372 )
30X-RAY DIFFRACTION30chain 'G' and (resid 373 through 395 )
31X-RAY DIFFRACTION31chain 'G' and (resid 396 through 404 )
32X-RAY DIFFRACTION32chain 'G' and (resid 405 through 433 )
33X-RAY DIFFRACTION33chain 'G' and (resid 434 through 454 )
34X-RAY DIFFRACTION34chain 'H' and (resid 346 through 372 )
35X-RAY DIFFRACTION35chain 'H' and (resid 373 through 453 )
36X-RAY DIFFRACTION36chain 'I' and (resid 1 through 12 )
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 10 )
38X-RAY DIFFRACTION38chain 'K' and (resid 1 through 11 )
39X-RAY DIFFRACTION39chain 'L' and (resid 1 through 8 )

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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

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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

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