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- PDB-6m8p: Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013 -

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基本情報

登録情報
データベース: PDB / ID: 6m8p
タイトルHuman ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013
要素Endoplasmic reticulum aminopeptidase 1
キーワードHYDROLASE/INHIBITOR / Inhibitor / Aminopeptidase / Antigen processing / HYDROLASE / HYDROLASE-INHIBITOR complex
機能・相同性
機能・相同性情報


interleukin-1, type II receptor binding / interleukin-6 receptor binding / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アミノペプチターゼ / metalloexopeptidase activity / regulation of innate immune response / peptide catabolic process / fat cell differentiation / metalloaminopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アミノペプチターゼ / metalloexopeptidase activity / regulation of innate immune response / peptide catabolic process / fat cell differentiation / metalloaminopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / membrane protein ectodomain proteolysis / aminopeptidase activity / peptide binding / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / membrane / cytoplasm / cytosol
類似検索 - 分子機能
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
類似検索 - ドメイン・相同性
Chem-P52 / Endoplasmic reticulum aminopeptidase 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.31 Å
データ登録者Maben, Z. / Stern, L.J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI038996 米国
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism.
著者: Maben, Z. / Arya, R. / Georgiadis, D. / Stratikos, E. / Stern, L.J.
履歴
登録2018年8月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年12月18日Provider: repository / タイプ: Initial release
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn
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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.d_res_low / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12022年6月1日Group: Database references / Structure summary
カテゴリ: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22023年10月11日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 2.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Endoplasmic reticulum aminopeptidase 1
B: Endoplasmic reticulum aminopeptidase 1
C: Endoplasmic reticulum aminopeptidase 1
D: Endoplasmic reticulum aminopeptidase 1
E: Endoplasmic reticulum aminopeptidase 1
F: Endoplasmic reticulum aminopeptidase 1
G: Endoplasmic reticulum aminopeptidase 1
H: Endoplasmic reticulum aminopeptidase 1
I: Endoplasmic reticulum aminopeptidase 1
J: Endoplasmic reticulum aminopeptidase 1
K: Endoplasmic reticulum aminopeptidase 1
L: Endoplasmic reticulum aminopeptidase 1
M: Endoplasmic reticulum aminopeptidase 1
N: Endoplasmic reticulum aminopeptidase 1
O: Endoplasmic reticulum aminopeptidase 1
P: Endoplasmic reticulum aminopeptidase 1
Q: Endoplasmic reticulum aminopeptidase 1
R: Endoplasmic reticulum aminopeptidase 1
S: Endoplasmic reticulum aminopeptidase 1
T: Endoplasmic reticulum aminopeptidase 1
U: Endoplasmic reticulum aminopeptidase 1
V: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,338,352441
ポリマ－2,265,27922
非ポリマー73,074419
水00
1
A: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,18819
ポリマ－102,9671
非ポリマー3,22118
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,38021
ポリマ－102,9671
非ポリマー3,41320
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,18819
ポリマ－102,9671
非ポリマー3,22118
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,47722
ポリマ－102,9671
非ポリマー3,50921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
12
L: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
13
M: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,38021
ポリマ－102,9671
非ポリマー3,41320
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
14
N: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
15
O: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
16
P: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,18819
ポリマ－102,9671
非ポリマー3,22118
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
17
Q: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,18819
ポリマ－102,9671
非ポリマー3,22118
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
18
R: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,38021
ポリマ－102,9671
非ポリマー3,41320
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
19
S: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
20
T: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,28420
ポリマ－102,9671
非ポリマー3,31719
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
21
U: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,38021
ポリマ－102,9671
非ポリマー3,41320
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
22
V: Endoplasmic reticulum aminopeptidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,18819
ポリマ－102,9671
非ポリマー3,22118
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)125.790, 548.684, 589.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
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
151
161
171
181
191
201
211
221

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE(chain 'A' and (resid 46 through 76 or resid 78...AA46 - 7630 - 60
12GLYGLYLYSLYS(chain 'A' and (resid 46 through 76 or resid 78...AA78 - 10962 - 93
13LEULEULEULEU(chain 'A' and (resid 46 through 76 or resid 78...AA115 - 28399 - 267
14ALAALALYSLYS(chain 'A' and (resid 46 through 76 or resid 78...AA285 - 526269 - 510
15ASPASPLEULEU(chain 'A' and (resid 46 through 76 or resid 78...AA533 - 709517 - 693
16VALVALPROPRO(chain 'A' and (resid 46 through 76 or resid 78...AA712 - 717696 - 701
17VALVALGLUGLU(chain 'A' and (resid 46 through 76 or resid 78...AA719 - 914703 - 898
21PROPROPHEPHE(chain 'B' and (resid 46 through 76 or resid 78...BB46 - 7630 - 60
22GLYGLYLYSLYS(chain 'B' and (resid 46 through 76 or resid 78...BB78 - 10962 - 93
23LEULEULEULEU(chain 'B' and (resid 46 through 76 or resid 78...BB115 - 28399 - 267
24ALAALALYSLYS(chain 'B' and (resid 46 through 76 or resid 78...BB285 - 526269 - 510
25ASPASPLEULEU(chain 'B' and (resid 46 through 76 or resid 78...BB533 - 709517 - 693
26VALVALPROPRO(chain 'B' and (resid 46 through 76 or resid 78...BB712 - 717696 - 701
27VALVALGLUGLU(chain 'B' and (resid 46 through 76 or resid 78...BB719 - 914703 - 898
31PROPROPHEPHE(chain 'C' and (resid 46 through 76 or resid 78...CC46 - 7630 - 60
32GLYGLYLYSLYS(chain 'C' and (resid 46 through 76 or resid 78...CC78 - 10962 - 93
33LEULEULEULEU(chain 'C' and (resid 46 through 76 or resid 78...CC115 - 28399 - 267
34ALAALALYSLYS(chain 'C' and (resid 46 through 76 or resid 78...CC285 - 526269 - 510
35ASPASPLEULEU(chain 'C' and (resid 46 through 76 or resid 78...CC533 - 709517 - 693
36VALVALPROPRO(chain 'C' and (resid 46 through 76 or resid 78...CC712 - 717696 - 701
37VALVALGLUGLU(chain 'C' and (resid 46 through 76 or resid 78...CC719 - 914703 - 898
41PROPROPHEPHE(chain 'D' and (resid 46 through 76 or resid 78...DD46 - 7630 - 60
42GLYGLYLYSLYS(chain 'D' and (resid 46 through 76 or resid 78...DD78 - 10962 - 93
43LEULEULEULEU(chain 'D' and (resid 46 through 76 or resid 78...DD115 - 28399 - 267
44ALAALALYSLYS(chain 'D' and (resid 46 through 76 or resid 78...DD285 - 526269 - 510
45ASPASPLEULEU(chain 'D' and (resid 46 through 76 or resid 78...DD533 - 709517 - 693
46VALVALPROPRO(chain 'D' and (resid 46 through 76 or resid 78...DD712 - 717696 - 701
47VALVALGLUGLU(chain 'D' and (resid 46 through 76 or resid 78...DD719 - 914703 - 898
51PROPROPHEPHE(chain 'E' and (resid 46 through 76 or resid 78...EE46 - 7630 - 60
52GLYGLYLYSLYS(chain 'E' and (resid 46 through 76 or resid 78...EE78 - 10962 - 93
53LEULEULEULEU(chain 'E' and (resid 46 through 76 or resid 78...EE115 - 28399 - 267
54ALAALALYSLYS(chain 'E' and (resid 46 through 76 or resid 78...EE285 - 526269 - 510
55ASPASPLEULEU(chain 'E' and (resid 46 through 76 or resid 78...EE533 - 709517 - 693
56VALVALPROPRO(chain 'E' and (resid 46 through 76 or resid 78...EE712 - 717696 - 701
57VALVALGLUGLU(chain 'E' and (resid 46 through 76 or resid 78...EE719 - 914703 - 898
61PROPROPHEPHE(chain 'F' and (resid 46 through 76 or resid 78...FF46 - 7630 - 60
62GLYGLYLYSLYS(chain 'F' and (resid 46 through 76 or resid 78...FF78 - 10962 - 93
63LEULEULEULEU(chain 'F' and (resid 46 through 76 or resid 78...FF115 - 28399 - 267
64ALAALALYSLYS(chain 'F' and (resid 46 through 76 or resid 78...FF285 - 526269 - 510
65ASPASPLEULEU(chain 'F' and (resid 46 through 76 or resid 78...FF533 - 709517 - 693
66VALVALPROPRO(chain 'F' and (resid 46 through 76 or resid 78...FF712 - 717696 - 701
67VALVALGLUGLU(chain 'F' and (resid 46 through 76 or resid 78...FF719 - 914703 - 898
71PROPROPHEPHE(chain 'G' and (resid 46 through 76 or resid 78...GG46 - 7630 - 60
72GLYGLYLYSLYS(chain 'G' and (resid 46 through 76 or resid 78...GG78 - 10962 - 93
73LEULEULEULEU(chain 'G' and (resid 46 through 76 or resid 78...GG115 - 28399 - 267
74ALAALALYSLYS(chain 'G' and (resid 46 through 76 or resid 78...GG285 - 526269 - 510
75ASPASPLEULEU(chain 'G' and (resid 46 through 76 or resid 78...GG533 - 709517 - 693
76VALVALPROPRO(chain 'G' and (resid 46 through 76 or resid 78...GG712 - 717696 - 701
77VALVALGLUGLU(chain 'G' and (resid 46 through 76 or resid 78...GG719 - 914703 - 898
81PROPROPHEPHE(chain 'H' and (resid 46 through 76 or resid 78...HH46 - 7630 - 60
82GLYGLYLYSLYS(chain 'H' and (resid 46 through 76 or resid 78...HH78 - 10962 - 93
83LEULEULEULEU(chain 'H' and (resid 46 through 76 or resid 78...HH115 - 28399 - 267
84ALAALALYSLYS(chain 'H' and (resid 46 through 76 or resid 78...HH285 - 526269 - 510
85ASPASPLEULEU(chain 'H' and (resid 46 through 76 or resid 78...HH533 - 709517 - 693
86VALVALPROPRO(chain 'H' and (resid 46 through 76 or resid 78...HH712 - 717696 - 701
87VALVALGLUGLU(chain 'H' and (resid 46 through 76 or resid 78...HH719 - 914703 - 898
91PROPROPHEPHE(chain 'I' and (resid 46 through 76 or resid 78...II46 - 7630 - 60
92GLYGLYLYSLYS(chain 'I' and (resid 46 through 76 or resid 78...II78 - 10962 - 93
93LEULEULEULEU(chain 'I' and (resid 46 through 76 or resid 78...II115 - 28399 - 267
94ALAALALYSLYS(chain 'I' and (resid 46 through 76 or resid 78...II285 - 526269 - 510
95ASPASPLEULEU(chain 'I' and (resid 46 through 76 or resid 78...II533 - 709517 - 693
96VALVALPROPRO(chain 'I' and (resid 46 through 76 or resid 78...II712 - 717696 - 701
97VALVALGLUGLU(chain 'I' and (resid 46 through 76 or resid 78...II719 - 914703 - 898
101PROPROPHEPHE(chain 'J' and (resid 46 through 76 or resid 78...JJ46 - 7630 - 60
102GLYGLYLYSLYS(chain 'J' and (resid 46 through 76 or resid 78...JJ78 - 10962 - 93
103LEULEULEULEU(chain 'J' and (resid 46 through 76 or resid 78...JJ115 - 28399 - 267
104ALAALALYSLYS(chain 'J' and (resid 46 through 76 or resid 78...JJ285 - 526269 - 510
105ASPASPLEULEU(chain 'J' and (resid 46 through 76 or resid 78...JJ533 - 709517 - 693
106VALVALPROPRO(chain 'J' and (resid 46 through 76 or resid 78...JJ712 - 717696 - 701
107VALVALGLUGLU(chain 'J' and (resid 46 through 76 or resid 78...JJ719 - 914703 - 898
111PROPROPHEPHE(chain 'K' and (resid 46 through 76 or resid 78...KK46 - 7630 - 60
112GLYGLYLYSLYS(chain 'K' and (resid 46 through 76 or resid 78...KK78 - 10962 - 93
113LEULEULEULEU(chain 'K' and (resid 46 through 76 or resid 78...KK115 - 28399 - 267
114ALAALALYSLYS(chain 'K' and (resid 46 through 76 or resid 78...KK285 - 526269 - 510
115ASPASPLEULEU(chain 'K' and (resid 46 through 76 or resid 78...KK533 - 709517 - 693
116VALVALPROPRO(chain 'K' and (resid 46 through 76 or resid 78...KK712 - 717696 - 701
117VALVALGLUGLU(chain 'K' and (resid 46 through 76 or resid 78...KK719 - 914703 - 898
121PROPROPHEPHE(chain 'L' and (resid 46 through 76 or resid 78...LL46 - 7630 - 60
122GLYGLYLYSLYS(chain 'L' and (resid 46 through 76 or resid 78...LL78 - 10962 - 93
123LEULEULEULEU(chain 'L' and (resid 46 through 76 or resid 78...LL115 - 28399 - 267
124ALAALALYSLYS(chain 'L' and (resid 46 through 76 or resid 78...LL285 - 526269 - 510
125ASPASPLEULEU(chain 'L' and (resid 46 through 76 or resid 78...LL533 - 709517 - 693
126VALVALPROPRO(chain 'L' and (resid 46 through 76 or resid 78...LL712 - 717696 - 701
127VALVALGLUGLU(chain 'L' and (resid 46 through 76 or resid 78...LL719 - 914703 - 898
131PROPROPHEPHE(chain 'M' and (resid 46 through 76 or resid 78...MM46 - 7630 - 60
132GLYGLYLYSLYS(chain 'M' and (resid 46 through 76 or resid 78...MM78 - 10962 - 93
133LEULEULEULEU(chain 'M' and (resid 46 through 76 or resid 78...MM115 - 28399 - 267
134ALAALALYSLYS(chain 'M' and (resid 46 through 76 or resid 78...MM285 - 526269 - 510
135ASPASPLEULEU(chain 'M' and (resid 46 through 76 or resid 78...MM533 - 709517 - 693
136VALVALPROPRO(chain 'M' and (resid 46 through 76 or resid 78...MM712 - 717696 - 701
137VALVALGLUGLU(chain 'M' and (resid 46 through 76 or resid 78...MM719 - 914703 - 898
141PROPROPHEPHE(chain 'N' and (resid 46 through 76 or resid 78...NN46 - 7630 - 60
142GLYGLYLYSLYS(chain 'N' and (resid 46 through 76 or resid 78...NN78 - 10962 - 93
143LEULEULEULEU(chain 'N' and (resid 46 through 76 or resid 78...NN115 - 28399 - 267
144ALAALALYSLYS(chain 'N' and (resid 46 through 76 or resid 78...NN285 - 526269 - 510
145ASPASPLEULEU(chain 'N' and (resid 46 through 76 or resid 78...NN533 - 709517 - 693
146VALVALPROPRO(chain 'N' and (resid 46 through 76 or resid 78...NN712 - 717696 - 701
147VALVALGLUGLU(chain 'N' and (resid 46 through 76 or resid 78...NN719 - 914703 - 898
151PROPROPHEPHE(chain 'O' and (resid 46 through 76 or resid 78...OO46 - 7630 - 60
152GLYGLYLYSLYS(chain 'O' and (resid 46 through 76 or resid 78...OO78 - 10962 - 93
153LEULEULEULEU(chain 'O' and (resid 46 through 76 or resid 78...OO115 - 28399 - 267
154ALAALALYSLYS(chain 'O' and (resid 46 through 76 or resid 78...OO285 - 526269 - 510
155ASPASPLEULEU(chain 'O' and (resid 46 through 76 or resid 78...OO533 - 709517 - 693
156VALVALPROPRO(chain 'O' and (resid 46 through 76 or resid 78...OO712 - 717696 - 701
157VALVALGLUGLU(chain 'O' and (resid 46 through 76 or resid 78...OO719 - 914703 - 898
161PROPROPHEPHE(chain 'P' and (resid 46 through 76 or resid 78...PP46 - 7630 - 60
162GLYGLYLYSLYS(chain 'P' and (resid 46 through 76 or resid 78...PP78 - 10962 - 93
163LEULEULEULEU(chain 'P' and (resid 46 through 76 or resid 78...PP115 - 28399 - 267
164ALAALALYSLYS(chain 'P' and (resid 46 through 76 or resid 78...PP285 - 526269 - 510
165ASPASPLEULEU(chain 'P' and (resid 46 through 76 or resid 78...PP533 - 709517 - 693
166VALVALPROPRO(chain 'P' and (resid 46 through 76 or resid 78...PP712 - 717696 - 701
167VALVALGLUGLU(chain 'P' and (resid 46 through 76 or resid 78...PP719 - 914703 - 898
171PROPROPHEPHE(chain 'Q' and (resid 46 through 76 or resid 78...QQ46 - 7630 - 60
172GLYGLYLYSLYS(chain 'Q' and (resid 46 through 76 or resid 78...QQ78 - 10962 - 93
173LEULEULEULEU(chain 'Q' and (resid 46 through 76 or resid 78...QQ115 - 28399 - 267
174ALAALALYSLYS(chain 'Q' and (resid 46 through 76 or resid 78...QQ285 - 526269 - 510
175ASPASPLEULEU(chain 'Q' and (resid 46 through 76 or resid 78...QQ533 - 709517 - 693
176VALVALPROPRO(chain 'Q' and (resid 46 through 76 or resid 78...QQ712 - 717696 - 701
177VALVALGLUGLU(chain 'Q' and (resid 46 through 76 or resid 78...QQ719 - 914703 - 898
181PROPROPHEPHE(chain 'R' and (resid 46 through 76 or resid 78...RR46 - 7630 - 60
182GLYGLYLYSLYS(chain 'R' and (resid 46 through 76 or resid 78...RR78 - 10962 - 93
183LEULEULEULEU(chain 'R' and (resid 46 through 76 or resid 78...RR115 - 28399 - 267
184ALAALALYSLYS(chain 'R' and (resid 46 through 76 or resid 78...RR285 - 526269 - 510
185ASPASPLEULEU(chain 'R' and (resid 46 through 76 or resid 78...RR533 - 709517 - 693
186VALVALPROPRO(chain 'R' and (resid 46 through 76 or resid 78...RR712 - 717696 - 701
187VALVALGLUGLU(chain 'R' and (resid 46 through 76 or resid 78...RR719 - 914703 - 898
191PROPROPHEPHE(chain 'S' and (resid 46 through 76 or resid 78...SS46 - 7630 - 60
192GLYGLYLYSLYS(chain 'S' and (resid 46 through 76 or resid 78...SS78 - 10962 - 93
193LEULEULEULEU(chain 'S' and (resid 46 through 76 or resid 78...SS115 - 28399 - 267
194ALAALALYSLYS(chain 'S' and (resid 46 through 76 or resid 78...SS285 - 526269 - 510
195ASPASPLEULEU(chain 'S' and (resid 46 through 76 or resid 78...SS533 - 709517 - 693
196VALVALPROPRO(chain 'S' and (resid 46 through 76 or resid 78...SS712 - 717696 - 701
197VALVALGLUGLU(chain 'S' and (resid 46 through 76 or resid 78...SS719 - 914703 - 898
201PROPROPHEPHE(chain 'T' and (resid 46 through 76 or resid 78...TT46 - 7630 - 60
202GLYGLYLYSLYS(chain 'T' and (resid 46 through 76 or resid 78...TT78 - 10962 - 93
203LEULEULEULEU(chain 'T' and (resid 46 through 76 or resid 78...TT115 - 28399 - 267
204ALAALALYSLYS(chain 'T' and (resid 46 through 76 or resid 78...TT285 - 526269 - 510
205ASPASPLEULEU(chain 'T' and (resid 46 through 76 or resid 78...TT533 - 709517 - 693
206VALVALPROPRO(chain 'T' and (resid 46 through 76 or resid 78...TT712 - 717696 - 701
207VALVALGLUGLU(chain 'T' and (resid 46 through 76 or resid 78...TT719 - 914703 - 898
211PROPROPHEPHE(chain 'U' and (resid 46 through 76 or resid 78...UU46 - 7630 - 60
212GLYGLYLYSLYS(chain 'U' and (resid 46 through 76 or resid 78...UU78 - 10962 - 93
213LEULEULEULEU(chain 'U' and (resid 46 through 76 or resid 78...UU115 - 28399 - 267
214ALAALALYSLYS(chain 'U' and (resid 46 through 76 or resid 78...UU285 - 526269 - 510
215ASPASPLEULEU(chain 'U' and (resid 46 through 76 or resid 78...UU533 - 709517 - 693
216VALVALPROPRO(chain 'U' and (resid 46 through 76 or resid 78...UU712 - 717696 - 701
217VALVALGLUGLU(chain 'U' and (resid 46 through 76 or resid 78...UU719 - 914703 - 898
221PROPROPHEPHE(chain 'V' and (resid 46 through 76 or resid 78...VV46 - 7630 - 60
222GLYGLYLYSLYS(chain 'V' and (resid 46 through 76 or resid 78...VV78 - 10962 - 93
223LEULEULEULEU(chain 'V' and (resid 46 through 76 or resid 78...VV115 - 28399 - 267
224ALAALALYSLYS(chain 'V' and (resid 46 through 76 or resid 78...VV285 - 526269 - 510
225ASPASPLEULEU(chain 'V' and (resid 46 through 76 or resid 78...VV533 - 709517 - 693
226VALVALPROPRO(chain 'V' and (resid 46 through 76 or resid 78...VV712 - 717696 - 701
227VALVALGLUGLU(chain 'V' and (resid 46 through 76 or resid 78...VV719 - 914703 - 898

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要素

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タンパク質 , 1種, 22分子 ABCDEFGHIJKLMNOPQRSTUV

#1: タンパク質 ...
Endoplasmic reticulum aminopeptidase 1 / ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin- ...ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin-insensitive leucyl-specific aminopeptidase / PILS-AP / Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator


分子量: 102967.211 Da / 分子数: 22 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: Q9NZ08, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アミノペプチターゼ

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糖 , 2種, 66分子

#2: 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: 44 / 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
#6: 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: 22 / 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, 353分子

#3: 化合物...
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 22 / 由来タイプ: 合成 / 式: Zn
#4: 化合物...
ChemComp-P52 / Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide


分子量: 512.581 Da / 分子数: 22 / 由来タイプ: 合成 / 式: C27H37N4O4P
#5: 化合物...
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 309 / 由来タイプ: 合成 / 式: SO4

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詳細

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: 4.69 Å3/Da / 溶媒含有率: 73.75 % / 解説: barrel-shaped, 200um diameter, 600um long
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5 / 詳細: 1.3M Ammonium sulfate, 100mM MES

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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-II / ビームライン: 17-ID-2 / 波長: 0.979 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年6月9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: 0.979 Å / 相対比: 1
反射解像度: 2.989→50.11 Å / Num. obs: 809932 / % possible obs: 99.1 % / 冗長度: 10.8 % / Biso Wilson estimate: 28.03 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 1.396 / Rpim(I) all: 0.645 / Rrim(I) all: 1.543 / Χ2: 1.13 / Net I/σ(I): 1.3
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.31-3.3710.85.5450.3294520.1392.5696.1271.0599.9
16.37-50.1111.30.1948.253000.9920.0830.2110.7296.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3211精密化
XDSJun 1, 2017データ削減
Aimless0.5.32データスケーリング
STARANISO1.9.6データスケーリング
PHASER2.8.0位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 2YD0

2yd0


解像度: 3.31→41.4 Å / SU ML: 0.4323 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 27.2909 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.2952 2123 0.47 %
Rwork0.2854 447908 -
obs0.2859 447829 74.69 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 39.46 Å2
精密化ステップサイクル: LAST / 解像度: 3.31→41.4 Å
タンパク質核酸リガンド溶媒全体
原子数151104 0 4383 0 155487
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0028159556
X-RAY DIFFRACTIONf_angle_d0.6047216892
X-RAY DIFFRACTIONf_chiral_restr0.043424244
X-RAY DIFFRACTIONf_plane_restr0.013426798
X-RAY DIFFRACTIONf_dihedral_angle_d13.156157470
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.390.4024220.32924907X-RAY DIFFRACTION12.42
3.39-3.470.3662400.33938295X-RAY DIFFRACTION20.94
3.47-3.570.349680.319813023X-RAY DIFFRACTION32.9
3.57-3.670.3648840.320118883X-RAY DIFFRACTION47.57
3.67-3.790.36121280.313724298X-RAY DIFFRACTION61.18
3.79-3.930.29581320.311629210X-RAY DIFFRACTION73.37
3.93-4.080.31931730.308333784X-RAY DIFFRACTION85.13
4.08-4.270.33371550.305137252X-RAY DIFFRACTION93.6
4.27-4.490.2791870.296238613X-RAY DIFFRACTION96.64
4.49-4.780.31351890.289439351X-RAY DIFFRACTION98.82
4.78-5.140.26731850.282639656X-RAY DIFFRACTION99.26
5.14-5.660.31091920.28739571X-RAY DIFFRACTION98.65
5.66-6.480.28461830.289639801X-RAY DIFFRACTION98.98
6.48-8.160.27411910.268340166X-RAY DIFFRACTION99.26
8.16-50.110.20611950.207841098X-RAY DIFFRACTION98.96
精密化 TLS手法: refined / Origin x: -94.1808649377 Å / Origin y: -392.743435873 Å / Origin z: 797.670350551 Å
111213212223313233
T0.19171266848 Å20.05243268245 Å2-0.0421600358816 Å2-0.291308374332 Å2-0.2363152019 Å2--0.240346582121 Å2
L-0.343731256564 °2-0.0414487663638 °2-0.00174090911546 °2--0.00626831844534 °2-0.0248621534321 °2--0.00648686000254 °2
S0.0940474645175 Å °-0.318799786187 Å °0.400119777069 Å °0.0424647813882 Å °-0.0414168822377 Å °0.0104839270131 Å °-0.0165604159326 Å °-0.0352866094496 Å °0.00289182505415 Å °
精密化 TLSグループSelection details: all

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る