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- PDB-2xwb: Crystal Structure of Complement C3b in complex with Factors B and D -

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基本情報

登録情報
データベース: PDB / ID: 2xwb
タイトルCrystal Structure of Complement C3b in complex with Factors B and D
要素
  • (COMPLEMENT C3B ...) x 2
  • (COMPLEMENT FACTOR ...) x 2
キーワードHYDROLASE / IMMUNE SYSTEM / PRO-CONVERTASE / SERINE PROTEASE / CONFORMATIONAL CHANGES / ALTERNATIVE PATHWAY
機能・相同性
機能・相同性情報


alternative-complement-pathway C3/C5 convertase / complement factor D / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation ...alternative-complement-pathway C3/C5 convertase / complement factor D / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement activation, GZMK pathway / positive regulation of G protein-coupled receptor signaling pathway / symbiont cell surface / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / complement activation, alternative pathway / complement activation / zymogen activation / neuron remodeling / endopeptidase inhibitor activity / B cell activation / amyloid-beta clearance / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / platelet alpha granule lumen / Regulation of Complement cascade / serine-type peptidase activity / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to bacterium / protein maturation / fatty acid metabolic process / positive regulation of protein phosphorylation / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / Platelet degranulation / secretory granule lumen / blood microparticle / G alpha (i) signalling events / ficolin-1-rich granule lumen / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / serine-type endopeptidase activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / : / extracellular exosome / extracellular region / plasma membrane
類似検索 - 分子機能
Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / Complement B/C2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 ...Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / Complement B/C2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Complement Module; domain 1 / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Glycosyltransferase - #20 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / von Willebrand factor, type A domain / Other non-globular / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / VWFA domain profile. / von Willebrand factor (vWF) type A domain / Single Sheet / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Special / Ribbon / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Complement factor D / Complement factor B / Complement C3
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.49 Å
データ登録者Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
引用ジャーナル: Science / 年: 2010
タイトル: Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.
著者: Forneris, F. / Ricklin, D. / Wu, J. / Tzekou, A. / Wallace, R.S. / Lambris, J.D. / Gros, P.
履歴
登録2010年11月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02011年1月12日Provider: repository / タイプ: Initial release
改定 1.12012年4月11日Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Version format compliance
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年12月20日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
H: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
J: COMPLEMENT FACTOR D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)566,82024
ポリマ－562,9878
非ポリマー3,83416
水724
1
A: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)283,51212
ポリマ－281,4934
非ポリマー2,0188
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18399 Å2
ΔGint-56.3 kcal/mol
Surface area107470 Å2
2
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
H: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)283,30912
ポリマ－281,4934
非ポリマー1,8158
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18198 Å2
ΔGint-60.7 kcal/mol
Surface area107122 Å2
3
C: COMPLEMENT C3B BETA CHAIN
D: COMPLEMENT C3B ALPHA' CHAIN
H: COMPLEMENT FACTOR B
J: COMPLEMENT FACTOR D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)283,30912
ポリマ－281,4934
非ポリマー1,8158
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20110 Å2
ΔGint-99.3 kcal/mol
Surface area131690 Å2
手法PISA
4
A: COMPLEMENT C3B BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
F: COMPLEMENT FACTOR B
I: COMPLEMENT FACTOR D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)283,51212
ポリマ－281,4934
非ポリマー2,0188
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-98.9 kcal/mol
Surface area131900 Å2
手法PISA
単位格子
Length a, b, c (Å)108.275, 135.775, 149.975
Angle α, β, γ (deg.)95.47, 110.69, 113.39
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A OR CHAIN B AND (RESSEQ 744:804 )
211CHAIN C OR CHAIN D AND (RESSEQ 744:804 )
112CHAIN B AND (RESSEQ 805:900 )
212CHAIN D AND (RESSEQ 805:900 )
113CHAIN B AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
213CHAIN D AND (RESSEQ 913:965 OR RESSEQ 1268:1331 )
114CHAIN B AND (RESSEQ 969:1102 )
214CHAIN D AND (RESSEQ 969:1102 )
115CHAIN B AND (RESSEQ 1108:1264 )
215CHAIN D AND (RESSEQ 1108:1264 )
116CHAIN B AND (RESSEQ 1332:1480 )
216CHAIN D AND (RESSEQ 1332:1480 )
117CHAIN B AND (RESSEQ 1485:1531 )
217CHAIN D AND (RESSEQ 1485:1531 )
118CHAIN B AND (RESSEQ 1538:1641 )
218CHAIN D AND (RESSEQ 1538:1641 )
119CHAIN F AND (RESSEQ 10:75 )
219CHAIN H AND (RESSEQ 10:75 )
1110CHAIN F AND (RESSEQ 78:220 )
2110CHAIN H AND (RESSEQ 78:220 )
1111CHAIN F AND (RESSEQ 244:340 )
2111CHAIN H AND (RESSEQ 244:340 )
1112CHAIN F AND (RESSEQ 358:460 )
2112CHAIN H AND (RESSEQ 358:460 )
1113CHAIN F AND (RESSEQ 485:741 )
2113CHAIN H AND (RESSEQ 485:741 )
1114CHAIN J
2114CHAIN I

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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要素

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COMPLEMENT C3B ... , 2種, 4分子 ACBD

#1: タンパク質 COMPLEMENT C3B BETA CHAIN


分子量: 71154.047 Da / 分子数: 2 / 断片: RESIDUES 23-664 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 器官: BLOOD / 組織: PLASMA / 参照: UniProt: P01024
#2: タンパク質 COMPLEMENT C3B ALPHA' CHAIN


分子量: 103759.797 Da / 分子数: 2 / 断片: RESIDUES 752-1663 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 器官: BLOOD / 組織: PLASMA / 参照: UniProt: P01024

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COMPLEMENT FACTOR ... , 2種, 4分子 FHIJ

#3: タンパク質 COMPLEMENT FACTOR B / C3/C5 CONVERTASE / GLYCINE-RICH BETA GLYCOPROTEIN / GBG / PBF2 / PROPERDIN FACTOR B


分子量: 82156.672 Da / 分子数: 2 / 断片: RESIDUES 35-764 / Mutation: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 組織: PLASMA / 器官: BLOOD / プラスミド: PUPE.06.08 / 細胞株 (発現宿主): HEK293-ES / 発現宿主: HOMO SAPIENS (ヒト)
参照: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#4: タンパク質 COMPLEMENT FACTOR D


分子量: 24422.807 Da / 分子数: 2 / Mutation: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 組織: PLASMA / 器官: BLOOD / プラスミド: PUPE.05.05 / 細胞株 (発現宿主): HEK293-ES / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: P00746, complement factor D

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糖 , 3種, 10分子

#5: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 5 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 3種, 10分子

#7: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg
#9: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 4 / 由来タイプ: 天然 / 式: H2O

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詳細

構成要素の詳細ENGINEERED RESIDUE IN CHAIN F, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN F, ASN 285 TO ASP ...ENGINEERED RESIDUE IN CHAIN F, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN F, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN H, ASP 279 TO GLY ENGINEERED RESIDUE IN CHAIN H, ASN 285 TO ASP ENGINEERED RESIDUE IN CHAIN I, SER 208 TO ALA ENGINEERED RESIDUE IN CHAIN J, SER 208 TO ALA
Has protein modificationY
配列の詳細RESIDUE 991 HAS BEEN CONVERTED FROM GLN TO GLU IN THE CONVERSION OF C3 TO C3B.

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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: 2

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試料調製

結晶マシュー密度: 3.29 Å3/Da / 溶媒含有率: 62.5 % / 解説: NONE
結晶化pH: 7.7 / 詳細: PH 7.7

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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: ESRF / ビームライン: ID23-1 / 波長: 0.8726
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2009年6月12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: 0.8726 Å / 相対比: 1
反射解像度: 3.5→67.42 Å / Num. obs: 88224 / % possible obs: 99.2 % / Observed criterion σ(I): 3.5 / 冗長度: 3.3 % / Biso Wilson estimate: 83.14 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8
反射 シェル解像度: 3.5→3.69 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE: 1.5_2)精密化
iMOSFLMデータ削減
SCALA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: PDB ENTRY 2A74

2a74


解像度: 3.49→65.95 Å / SU ML: 0.46 / σ(F): 2.01 / 位相誤差: 24.08 / 立体化学のターゲット値: ML
詳細: WATER MOLECULES HAVE BEEN INCLUDED ONLY TO COMPLETE THE COORDINATION OF THE MG2+ ION IN THE MIDAS SITE
Rfactor反射数%反射
Rfree0.244 4427 5 %
Rwork0.189 --
obs0.192 88180 98.6 %
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 / Bsol: 58.14 Å2 / ksol: 0.3 e/Å3
原子変位パラメータBiso mean: 114.37 Å2
Baniso -1Baniso -2Baniso -3
1--10.2414 Å211.8086 Å2-8.8541 Å2
2---4.0625 Å2-5.1292 Å2
3---2.7506 Å2
精密化ステップサイクル: LAST / 解像度: 3.49→65.95 Å
タンパク質核酸リガンド溶媒全体
原子数39033 0 248 4 39285
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00240171
X-RAY DIFFRACTIONf_angle_d0.48854375
X-RAY DIFFRACTIONf_dihedral_angle_d11.11114898
X-RAY DIFFRACTIONf_chiral_restr0.0576102
X-RAY DIFFRACTIONf_plane_restr0.0027022
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A5020X-RAY DIFFRACTIONPOSITIONAL
12C5020X-RAY DIFFRACTIONPOSITIONAL0.05
21B790X-RAY DIFFRACTIONPOSITIONAL
22D790X-RAY DIFFRACTIONPOSITIONAL0.027
31B908X-RAY DIFFRACTIONPOSITIONAL
32D908X-RAY DIFFRACTIONPOSITIONAL0.084
41B1048X-RAY DIFFRACTIONPOSITIONAL
42D1048X-RAY DIFFRACTIONPOSITIONAL0.026
51B1238X-RAY DIFFRACTIONPOSITIONAL
52D1238X-RAY DIFFRACTIONPOSITIONAL0.021
61B1133X-RAY DIFFRACTIONPOSITIONAL
62D1133X-RAY DIFFRACTIONPOSITIONAL0.02
71B370X-RAY DIFFRACTIONPOSITIONAL
72D370X-RAY DIFFRACTIONPOSITIONAL0.1
81B849X-RAY DIFFRACTIONPOSITIONAL
82D849X-RAY DIFFRACTIONPOSITIONAL0.028
91F509X-RAY DIFFRACTIONPOSITIONAL
92H509X-RAY DIFFRACTIONPOSITIONAL0.02
101F1115X-RAY DIFFRACTIONPOSITIONAL
102H1115X-RAY DIFFRACTIONPOSITIONAL0.027
111F752X-RAY DIFFRACTIONPOSITIONAL
112H752X-RAY DIFFRACTIONPOSITIONAL0.033
121F830X-RAY DIFFRACTIONPOSITIONAL
122H830X-RAY DIFFRACTIONPOSITIONAL0.029
131F2030X-RAY DIFFRACTIONPOSITIONAL
132H2030X-RAY DIFFRACTIONPOSITIONAL0.075
141J1710X-RAY DIFFRACTIONPOSITIONAL
142I1710X-RAY DIFFRACTIONPOSITIONAL0.026
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.493-3.53270.37371480.30022283X-RAY DIFFRACTION84
3.5327-3.57430.34611890.28552797X-RAY DIFFRACTION99
3.5743-3.61780.32841480.27122787X-RAY DIFFRACTION99
3.6178-3.66360.30961310.26272859X-RAY DIFFRACTION99
3.6636-3.71180.32341290.24722806X-RAY DIFFRACTION99
3.7118-3.76270.30771490.24422777X-RAY DIFFRACTION99
3.7627-3.81640.27531470.22312783X-RAY DIFFRACTION99
3.8164-3.87340.29411370.21792875X-RAY DIFFRACTION99
3.8734-3.93390.27511480.21132782X-RAY DIFFRACTION99
3.9339-3.99840.26111400.20172827X-RAY DIFFRACTION99
3.9984-4.06730.2241330.19422776X-RAY DIFFRACTION99
4.0673-4.14130.26331470.18292823X-RAY DIFFRACTION99
4.1413-4.22090.25861450.17072800X-RAY DIFFRACTION99
4.2209-4.30710.2081610.1672836X-RAY DIFFRACTION99
4.3071-4.40070.2481420.16192801X-RAY DIFFRACTION99
4.4007-4.5030.18791290.15282833X-RAY DIFFRACTION99
4.503-4.61560.20261360.14862777X-RAY DIFFRACTION99
4.6156-4.74040.2191350.14452860X-RAY DIFFRACTION99
4.7404-4.87980.20441670.14242806X-RAY DIFFRACTION99
4.8798-5.03730.18691800.14192775X-RAY DIFFRACTION99
5.0373-5.21730.19431540.14152798X-RAY DIFFRACTION99
5.2173-5.42610.19471520.15242815X-RAY DIFFRACTION99
5.4261-5.67290.22221590.15932810X-RAY DIFFRACTION99
5.6729-5.97180.2171440.16422820X-RAY DIFFRACTION99
5.9718-6.34570.1941330.1682801X-RAY DIFFRACTION99
6.3457-6.83510.25321510.17252838X-RAY DIFFRACTION99
6.8351-7.52210.23791420.17192810X-RAY DIFFRACTION99
7.5221-8.60850.23881410.16822808X-RAY DIFFRACTION100
8.6085-10.83810.1881600.15892813X-RAY DIFFRACTION99
10.8381-65.96580.24911500.222777X-RAY DIFFRACTION98
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05470.7499-0.30370.6370.25530.3580.3476-0.4663-0.45930.1559-0.1931-0.2842-0.19940.0552-0.16360.5829-0.21110.11370.6596-0.19071.202885.4108-95.20444.3835
21.17740.16130.61030.0291-0.02010.16190.00330.2054-0.399-0.0405-0.0380.1639-0.0951-0.01810.03330.3294-0.21470.0380.6374-0.25380.349469.5548-57.11710.1669
30.15590.0870.53422.1061.12532.02470.2741-0.7097-0.1416-0.3748-0.07660.806-0.2446-0.3597-0.08620.4395-0.3588-0.13751.008-0.17810.668145.033-51.1066-13.8188
40.71511.1130.39322.51640.46570.07430.11440.2294-0.1554-0.2356-0.32930.49690.1435-0.35150.18240.7433-0.4219-0.07341.1031-0.16871.117347.9218-85.3976-6.7193
51.20640.33570.4850.12980.28420.66910.4794-0.0399-0.94640.5186-0.3779-0.12940.1642-0.1263-0.14840.8906-0.50480.13440.7156-0.07221.410462.4122-97.6287.5642
63.12882.1764-0.49471.7983-0.84771.01850.09750.333-0.56850.12570.2231-0.4601-0.4648-0.3361-0.0950.5494-0.42130.39830.7903-0.17640.556657.5733-54.58624.7416
70.81510.2953-0.02430.8468-0.77980.7216-0.1715-0.3723-0.5320.32430.23080.07790.1922-0.39340.07770.0196-0.41660.05880.177-0.04650.381368.7179-74.4444.1703
80.9717-0.50550.30791.23970.1211-0.1550.14750.35770.1218-0.0738-0.13170.2941-0.0056-0.41370.11360.0698-0.07-0.01510.4852-0.1005-0.017769.0099-36.53156.0121
91.2230.3827-0.80781.82420.433.49330.15870.3566-0.2984-0.3296-0.13590.43910.296-0.4511-0.10990.43590.0322-0.15980.377-0.04380.4541110.7906-94.4691-23.1379
100.5420.36780.23480.33530.27530.92120.11910.7847-0.12090.1320.1439-0.4677-0.13770.027-0.04270.1980.00370.1690.867-0.11380.049294.64-45.2274-13.8302
111.10880.94021.40321.74790.38083.0042-0.22440.13950.4983-0.22060.03820.7436-0.0376-0.6050.15080.28130.0969-0.18720.90980.01010.515850.2976-20.7993-8.2497
121.55190.29360.30980.5748-0.76682.27440.080.0080.7896-0.1523-0.2741-0.0827-0.42720.15960.24240.70610.1383-0.25120.23960.09050.552379.25138.13883.5686
130.6298-0.0388-0.3541.00311.21231.54990.4330.37260.15750.81510.192-0.53080.0904-0.7271-0.67990.94690.34950.37230.40450.35661.3689156.3188-99.65962.5558
140.5099-0.171-0.10440.19860.15440.57110.0731-0.3865-0.4318-0.18420.2135-0.2904-0.34910.4290.39180.77240.6863-0.11680.44220.1560.2445157.4133-65.676177.6229
150.66760.4750.59830.4109-0.13712.10780.04210.3443-0.32850.20020.2615-0.3318-0.32680.1849-0.18520.46470.4783-0.17160.7896-0.10370.4067191.3676-58.923991.0558
160.1904-0.1522-0.15272.44650.41430.0823-0.0304-0.43970.0170.2705-0.1255-0.91660.23470.03630.10771.22460.5994-0.17931.0492-0.05971.132191.1889-87.072176.4315
171.9304-1.63740.3441.3275-0.2788-0.0481-0.0124-0.122-0.57050.2292-0.00960.4855-0.18710.19080.01710.94490.50350.22470.55810.05530.6843178.3102-95.901658.7406
180.4537-0.791-0.93811.41251.68121.99910.10350.1456-0.0181-0.239-0.3545-0.1094-0.1671-0.72060.20631.78190.45190.74851.77570.02751.4022180.2121-45.026455.547
190.2086-0.5774-0.3582.52710.56020.4154-0.3979-0.2291-0.2021-0.32870.323-0.0960.21780.21870.12710.72120.57140.0970.69770.05580.44170.0721-77.495169.8047
200.97450.2851-0.05870.49150.28120.63920.1188-0.51380.0728-0.00760.0430.00210.44740.7299-0.0610.47310.2853-0.07730.6614-0.03410.1317164.2821-42.12980.292
210.50310.49170.8162.348-0.02391.8080.15140.0494-0.0837-0.16340.32850.48290.4106-1.0805-0.44371.344-0.1590.09881.2850.07341.571134.3229-112.280290.9892
221-0.5578-0.28830.4381-0.08220.59050.0552-0.44980.0685-0.05990.24670.1441-0.17540.369-0.12360.3930.1165-0.01110.6270.13020.2333141.2915-58.941795.995
230.8076-0.6877-0.04081.25180.10290.9451-0.055-0.18210.18970.36980.0979-0.35390.18220.756-0.10320.24440.1284-0.10641.0097-0.21410.1892181.043-29.105199.1944
240.14-0.0418-0.00760.72630.80581.2401-0.0083-0.13670.18860.22150.2545-0.2910.16840.3513-0.21350.2796-0.0293-0.00720.3436-0.1810.26148.1977-1.620795.9749
252.1568-1.8331-0.42342.14410.45620.2881-0.10220.5858-0.70040.38840.11370.2499-0.5068-0.49330.17420.2960.1680.12420.6805-0.41660.584377.6498-2.110137.5645
260.5912-0.4551-0.11630.4077-0.05210.2502-0.2475-0.07850.07060.159-0.0010.0385-0.2869-0.50090.08960.55630.1978-0.09920.914-0.15080.53478.2876-6.924531.2691
272.999-0.3960.1610.94340.03180.0141-0.40710.0730.1384-0.42470.54460.14690.21940.7139-0.10551.23990.12420.08341.3028-0.30560.460671.6448-10.140122.5855
281.1661.54531.4722.53011.57482.2652-0.2927-0.1064-0.0119-0.0953-0.14950.47110.2786-1.02040.09880.2305-0.22440.04640.5230.02980.247475.8732-34.962824.8998
290.89910.3283-0.82940.4314-0.22550.8658-0.03540.29790.1595-0.3288-0.16990.08240.0079-0.9247-0.64380.1625-0.1250.17670.52570.10240.013486.7334-33.171614.3609
300.16260.10430.00720.621-0.03010.1731-0.2033-0.20460.06240.0187-0.16550.46570.0631-0.2674-0.87250.1794-0.27340.2785-0.21460.7024-0.1898105.4941-24.783623.2683
311.6935-0.3809-0.03542.11390.51721.38040.13940.42190.1471-0.3131-0.1993-0.1512-0.3876-0.2405-0.12420.3143-0.08290.04580.240.12670.0612104.7127-11.547818.0242
321.94110.42350.82591.06650.03871.4658-0.00360.3933-0.31670.00720.02480.02930.24370.3011-0.01780.1322-0.06980.08710.1926-0.07740.294114.4836-51.899311.9449
331.04361.45240.46272.27060.14451.2774-0.29240.13530.4558-0.1812-0.0915-0.6159-0.67770.88110.35660.5222-0.1875-0.09990.79240.09380.7982150.7397-5.09363.3619
342.0251.1939-2.1341.3146-1.16272.3168-0.33080.06950.46330.11710.5384-0.08430.7053-0.8843-0.08311.1582-0.3523-0.19941.5908-0.01790.6747157.7806-12.415672.5605
352.301-0.28650.41530.0414-0.04460.9463-0.03010.17250.07340.009-0.0123-0.07080.47221.05870.04970.30680.3289-0.06050.7128-0.14840.3049157.8688-32.900563.8362
360.45430.37940.30040.66220.28580.2273-0.34020.5203-0.11260.53110.58210.01910.28990.2003-0.21660.54040.34810.13670.8771-0.00980.3288149.974-41.074162.0204
371.3938-0.22940.11060.9313-0.09680.25650.0941-0.5692-0.05060.27220.1812-0.17790.51550.7364-0.16550.47410.16110.05610.5795-0.03070.0633145.3302-36.967676.5563
380.1696-0.2363-0.41240.85551.23181.88080.0188-0.07090.02910.4030.2013-0.00510.71740.12880.16510.20820.19770.1171-0.2983-0.5076-0.5283124.5662-31.194667.1208
391.0788-0.26230.52561.250.00650.74630.1278-0.2230.13390.1609-0.14540.06880.0407-0.10880.07030.30040.07460.10010.243-0.03810.0195125.5464-19.459574.9294
401.9911-0.09680.33070.42930.26821.73320.0357-0.1414-0.5466-0.20510.04770.1170.645-0.1108-0.07250.74270.0961-0.04710.1483-0.00260.5058121.1442-60.853668.7665
411.22240.40251.06060.32720.40291.6738-0.543-0.02490.656-0.1408-0.24260.0385-0.10030.00310.49160.4129-0.0514-0.04010.2903-0.19640.464592.1157-16.196353.8156
421.21840.1744-0.11240.1625-0.3671.1951-0.2462-0.61650.0937-0.0414-0.05960.01921.16960.22930.39160.91670.17070.1471.3197-0.12030.677488.6528-22.55770.1836
430.74090.16280.80751.43810.96852.5284-0.2523-0.25310.32450.0927-0.4491-0.0858-0.0692-0.79440.49840.27020.1402-0.03140.4306-0.19610.328391.1025-19.302753.1206
441.84021.13961.28920.82870.36881.960.4856-0.6633-0.27150.3668-0.2941-0.55480.6965-0.61980.17680.4008-0.00130.20460.3579-0.0478-0.162996.4693-32.043951.1088
450.61230.658-0.0640.7779-0.2331.4174-0.2-0.21550.12290.1876-0.2948-0.4463-0.51090.15420.36750.443-0.126-0.11320.44430.19070.5818138.0311-11.261640.283
462.0411-0.9110.65660.4169-0.2690.2688-0.14470.91760.26210.0155-0.4798-0.1986-0.0360.71790.49650.9887-0.29280.14011.47130.37981.1628141.9554-11.983722.8346
472.07660.48471.19051.0533-0.51731.4344-0.29480.39410.61630.1177-0.21010.0869-0.31930.27980.38090.1992-0.1309-0.030.22190.08160.3015137.4753-18.794739.6939
480.30570.20590.36150.68630.41750.42810.4802-0.1693-0.00730.29-0.61480.22610.24220.1249-0.06070.4761-0.07040.08530.43810.26670.0364138.7125-25.884436.6109
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:105)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 106:245)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 246:317)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 318:431)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 432:539)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 540:552)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 553:642)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 730:966)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 967:1266)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 1267:1334)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1335:1499)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 1500:1641)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 1:105)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 106:207)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 208:310)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 311:442)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 443:545)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 546:551)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 552:642)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 730:966)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 967:1267)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 1268:1336)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 1337:1499)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 1500:1641)
25X-RAY DIFFRACTION25(CHAIN F AND RESID 10:30)
26X-RAY DIFFRACTION26(CHAIN F AND RESID 31:62)
27X-RAY DIFFRACTION27(CHAIN F AND RESID 63:70)
28X-RAY DIFFRACTION28(CHAIN F AND RESID 71:108)
29X-RAY DIFFRACTION29(CHAIN F AND RESID 109:198)
30X-RAY DIFFRACTION30(CHAIN F AND RESID 199:223)
31X-RAY DIFFRACTION31(CHAIN F AND RESID 240:447)
32X-RAY DIFFRACTION32(CHAIN F AND RESID 448:741)
33X-RAY DIFFRACTION33(CHAIN H AND RESID 10:62)
34X-RAY DIFFRACTION34(CHAIN H AND RESID 63:70)
35X-RAY DIFFRACTION35(CHAIN H AND RESID 71:96)
36X-RAY DIFFRACTION36(CHAIN H AND RESID 97:136)
37X-RAY DIFFRACTION37(CHAIN H AND RESID 137:200)
38X-RAY DIFFRACTION38(CHAIN H AND RESID 201:223)
39X-RAY DIFFRACTION39(CHAIN H AND RESID 240:451)
40X-RAY DIFFRACTION40(CHAIN H AND RESID 452:741)
41X-RAY DIFFRACTION41(CHAIN I AND RESID 1:42)
42X-RAY DIFFRACTION42(CHAIN I AND RESID 43:48)
43X-RAY DIFFRACTION43(CHAIN I AND RESID 49:150)
44X-RAY DIFFRACTION44(CHAIN I AND RESID 151:228)
45X-RAY DIFFRACTION45(CHAIN J AND RESID 1:42)
46X-RAY DIFFRACTION46(CHAIN J AND RESID 43:48)
47X-RAY DIFFRACTION47(CHAIN J AND RESID 49:197)
48X-RAY DIFFRACTION48(CHAIN J AND RESID 198:227)

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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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