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

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Basic information

Entry
Database: PDB / ID: 6m8p
TitleHuman ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013
ComponentsEndoplasmic reticulum aminopeptidase 1ERAP1
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Aminopeptidase / Antigen processing / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / regulation of innate immune response / peptide catabolic process / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / regulation of innate immune response / peptide catabolic process / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / zinc ion binding / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / 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.
Similarity search - Domain/homology
Chem-P52 / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsMaben, Z. / Stern, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI038996 United States
CitationJournal: Nat Commun / Year: 2021
Title: Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism.
Authors: Maben, Z. / Arya, R. / Georgiadis, D. / Stratikos, E. / Stern, L.J.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 1, 2022Group: Database references / Structure summary
Category: 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
Revision 2.2Oct 11, 2023Group: Data collection / Refinement description
Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,338,352441
Polymers2,265,27922
Non-polymers73,074419
Water0
1
A: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18819
Polymers102,9671
Non-polymers3,22118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,38021
Polymers102,9671
Non-polymers3,41320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18819
Polymers102,9671
Non-polymers3,22118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,47722
Polymers102,9671
Non-polymers3,50921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,38021
Polymers102,9671
Non-polymers3,41320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18819
Polymers102,9671
Non-polymers3,22118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18819
Polymers102,9671
Non-polymers3,22118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,38021
Polymers102,9671
Non-polymers3,41320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
S: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
T: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,28420
Polymers102,9671
Non-polymers3,31719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
U: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,38021
Polymers102,9671
Non-polymers3,41320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
V: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18819
Polymers102,9671
Non-polymers3,22118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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)
Noncrystallographic symmetry (NCS)NCS domain:
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 domain segments:

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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Components

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Protein , 1 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUV

#1: Protein ...
Endoplasmic reticulum aminopeptidase 1 / ERAP1 / 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


Mass: 102967.211 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Sugars , 2 types, 66 molecules

#2: Polysaccharide...
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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 44
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
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: Sugar...
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
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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Non-polymers , 3 types, 353 molecules

#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-P52 / Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide


Mass: 512.581 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C27H37N4O4P
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 309 / Source method: obtained synthetically / Formula: SO4

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.75 % / Description: barrel-shaped, 200um diameter, 600um long
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.3M Ammonium sulfate, 100mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.989→50.11 Å / Num. obs: 809932 / % possible obs: 99.1 % / Redundancy: 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
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)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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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSJun 1, 2017data reduction
Aimless0.5.32data scaling
STARANISO1.9.6data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD0

2yd0


Resolution: 3.31→41.4 Å / SU ML: 0.4323 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.2909 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2952 2123 0.47 %
Rwork0.2854 447908 -
obs0.2859 447829 74.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.46 Å2
Refinement stepCycle: LAST / Resolution: 3.31→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms151104 0 4383 0 155487
Refine LS restraints
Refine-IDTypeDev idealNumber
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 refinement shell
Resolution (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
Refinement TLS params.Method: 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 °
Refinement TLS groupSelection details: all

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