data_2VF8
#
_model_server_result.job_id            KnGHNObrbsgN9_Mwpp4oqA 
_model_server_result.datetime_utc      '2024-11-05 00:22:43' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          2vf8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1844}' 
#
_entry.id    2VF8 
#
_exptl.entry_id    2VF8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            2VF8 
_cell.length_a            149.632 
_cell.length_b            171.04 
_cell.length_c            204.205 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VF8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PQS monomeric 1 software_defined_assembly 2 
PQS monomeric 1 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 1 
A,C,D,E,F,G,H,I,T 2 1 
B,J,K,L,M,N,O,P,Q,R,S,U 3 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 J N N 
? 2 K N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.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.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A SG CYS 151 A CYS 151 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc2 A SG CYS 154 A CYS 154 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc3 A SG CYS 287 A CYS 287 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc4 A SG CYS 290 A CYS 290 1_555 E ZN ZN . A ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc5 A SG CYS 641 A CYS 641 1_555 F ZN ZN . A ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc6 B SG CYS 151 B CYS 151 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc7 B SG CYS 154 B CYS 154 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc8 B SG CYS 287 B CYS 287 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? 
metalc ? metalc9 B SG CYS 290 B CYS 290 1_555 L ZN ZN . B ZN 1845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc10 B SG CYS 641 B CYS 641 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc11 B SG CYS 644 B CYS 644 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc12 B SG CYS 664 B CYS 664 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc13 B SG CYS 667 B CYS 667 1_555 M ZN ZN . B ZN 1846 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     2VF8 
_atom_sites.fract_transf_matrix[1][1]    0.006683 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005847 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.004897 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 ADP A 1 1843 1843 ADP ADP . 
D 2 ADP A 1 1844 1844 ADP ADP . 
E 3 ZN A 1 1845 1845 ZN ZN . 
F 3 ZN A 1 1846 1846 ZN ZN . 
G 4 SO4 A 1 1847 1847 SO4 SO4 . 
H 4 SO4 A 1 1848 1848 SO4 SO4 . 
I 4 SO4 A 1 1849 1849 SO4 SO4 . 
J 2 ADP B 1 1843 1843 ADP ADP . 
K 2 ADP B 1 1844 1844 ADP ADP . 
L 3 ZN B 1 1845 1845 ZN ZN . 
M 3 ZN B 1 1846 1846 ZN ZN . 
N 4 SO4 B 1 1847 1847 SO4 SO4 . 
O 4 SO4 B 1 1848 1848 SO4 SO4 . 
P 4 SO4 B 1 1849 1849 SO4 SO4 . 
Q 4 SO4 B 1 1850 1850 SO4 SO4 . 
R 4 SO4 B 1 1851 1851 SO4 SO4 . 
S 5 PO4 B 1 1852 1852 PO4 PO4 . 
T 6 HOH A 1 2001 2001 HOH HOH . 
T 6 HOH A 2 2002 2002 HOH HOH . 
T 6 HOH A 3 2003 2003 HOH HOH . 
T 6 HOH A 4 2004 2004 HOH HOH . 
T 6 HOH A 5 2005 2005 HOH HOH . 
T 6 HOH A 6 2006 2006 HOH HOH . 
T 6 HOH A 7 2007 2007 HOH HOH . 
T 6 HOH A 8 2008 2008 HOH HOH . 
T 6 HOH A 9 2009 2009 HOH HOH . 
T 6 HOH A 10 2010 2010 HOH HOH . 
T 6 HOH A 11 2011 2011 HOH HOH . 
T 6 HOH A 12 2012 2012 HOH HOH . 
T 6 HOH A 13 2013 2013 HOH HOH . 
T 6 HOH A 14 2014 2014 HOH HOH . 
T 6 HOH A 15 2015 2015 HOH HOH . 
T 6 HOH A 16 2016 2016 HOH HOH . 
T 6 HOH A 17 2017 2017 HOH HOH . 
T 6 HOH A 18 2018 2018 HOH HOH . 
T 6 HOH A 19 2019 2019 HOH HOH . 
T 6 HOH A 20 2020 2020 HOH HOH . 
T 6 HOH A 21 2021 2021 HOH HOH . 
T 6 HOH A 22 2022 2022 HOH HOH . 
T 6 HOH A 23 2023 2023 HOH HOH . 
T 6 HOH A 24 2024 2024 HOH HOH . 
T 6 HOH A 25 2025 2025 HOH HOH . 
T 6 HOH A 26 2026 2026 HOH HOH . 
T 6 HOH A 27 2027 2027 HOH HOH . 
T 6 HOH A 28 2028 2028 HOH HOH . 
T 6 HOH A 29 2029 2029 HOH HOH . 
T 6 HOH A 30 2030 2030 HOH HOH . 
T 6 HOH A 31 2031 2031 HOH HOH . 
T 6 HOH A 32 2032 2032 HOH HOH . 
T 6 HOH A 33 2033 2033 HOH HOH . 
T 6 HOH A 34 2034 2034 HOH HOH . 
T 6 HOH A 35 2035 2035 HOH HOH . 
T 6 HOH A 36 2036 2036 HOH HOH . 
T 6 HOH A 37 2037 2037 HOH HOH . 
U 6 HOH B 1 2001 2001 HOH HOH . 
U 6 HOH B 2 2002 2002 HOH HOH . 
U 6 HOH B 3 2003 2003 HOH HOH . 
U 6 HOH B 4 2004 2004 HOH HOH . 
U 6 HOH B 5 2005 2005 HOH HOH . 
U 6 HOH B 6 2006 2006 HOH HOH . 
U 6 HOH B 7 2007 2007 HOH HOH . 
U 6 HOH B 8 2008 2008 HOH HOH . 
U 6 HOH B 9 2009 2009 HOH HOH . 
U 6 HOH B 10 2010 2010 HOH HOH . 
U 6 HOH B 11 2011 2011 HOH HOH . 
U 6 HOH B 12 2012 2012 HOH HOH . 
U 6 HOH B 13 2013 2013 HOH HOH . 
U 6 HOH B 14 2014 2014 HOH HOH . 
U 6 HOH B 15 2015 2015 HOH HOH . 
U 6 HOH B 16 2016 2016 HOH HOH . 
U 6 HOH B 17 2017 2017 HOH HOH . 
U 6 HOH B 18 2018 2018 HOH HOH . 
U 6 HOH B 19 2019 2019 HOH HOH . 
U 6 HOH B 20 2020 2020 HOH HOH . 
U 6 HOH B 21 2021 2021 HOH HOH . 
U 6 HOH B 22 2022 2022 HOH HOH . 
U 6 HOH B 23 2023 2023 HOH HOH . 
U 6 HOH B 24 2024 2024 HOH HOH . 
U 6 HOH B 25 2025 2025 HOH HOH . 
U 6 HOH B 26 2026 2026 HOH HOH . 
U 6 HOH B 27 2027 2027 HOH HOH . 
U 6 HOH B 28 2028 2028 HOH HOH . 
U 6 HOH B 29 2029 2029 HOH HOH . 
U 6 HOH B 30 2030 2030 HOH HOH . 
U 6 HOH B 31 2031 2031 HOH HOH . 
U 6 HOH B 32 2032 2032 HOH HOH . 
U 6 HOH B 33 2033 2033 HOH HOH . 
U 6 HOH B 34 2034 2034 HOH HOH . 
U 6 HOH B 35 2035 2035 HOH HOH . 
U 6 HOH B 36 2036 2036 HOH HOH . 
U 6 HOH B 37 2037 2037 HOH HOH . 
U 6 HOH B 38 2038 2038 HOH HOH . 
U 6 HOH B 39 2039 2039 HOH HOH . 
U 6 HOH B 40 2040 2040 HOH HOH . 
U 6 HOH B 41 2041 2041 HOH HOH . 
U 6 HOH B 42 2042 2042 HOH HOH . 
U 6 HOH B 43 2043 2043 HOH HOH . 
U 6 HOH B 44 2044 2044 HOH HOH . 
U 6 HOH B 45 2045 2045 HOH HOH . 
U 6 HOH B 46 2046 2046 HOH HOH . 
U 6 HOH B 47 2047 2047 HOH HOH . 
U 6 HOH B 48 2048 2048 HOH HOH . 
U 6 HOH B 49 2049 2049 HOH HOH . 
U 6 HOH B 50 2050 2050 HOH HOH . 
U 6 HOH B 51 2051 2051 HOH HOH . 
U 6 HOH B 52 2052 2052 HOH HOH . 
U 6 HOH B 53 2053 2053 HOH HOH . 
U 6 HOH B 54 2054 2054 HOH HOH . 
U 6 HOH B 55 2055 2055 HOH HOH . 
U 6 HOH B 56 2056 2056 HOH HOH . 
U 6 HOH B 57 2057 2057 HOH HOH . 
U 6 HOH B 58 2058 2058 HOH HOH . 
U 6 HOH B 59 2059 2059 HOH HOH . 
U 6 HOH B 60 2060 2060 HOH HOH . 
U 6 HOH B 61 2061 2061 HOH HOH . 
U 6 HOH B 62 2062 2062 HOH HOH . 
U 6 HOH B 63 2063 2063 HOH HOH . 
U 6 HOH B 64 2064 2064 HOH HOH . 
U 6 HOH B 65 2065 2065 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PB ADP . . . D 2 74.033 125.884 110.078 1 32.2 ? PB ADP 1844 A 1 
HETATM 2 O O1B ADP . . . D 2 73.405 126.265 108.744 1 31.3 ? O1B ADP 1844 A 1 
HETATM 3 O O2B ADP . . . D 2 72.96 125.823 111.1 1 33.22 ? O2B ADP 1844 A 1 
HETATM 4 O O3B ADP . . . D 2 75.328 126.49 110.521 1 32.18 ? O3B ADP 1844 A 1 
HETATM 5 P PA ADP . . . D 2 73.69 123.027 109.937 1 31.77 ? PA ADP 1844 A 1 
HETATM 6 O O1A ADP . . . D 2 72.354 123.284 109.301 1 34.9 ? O1A ADP 1844 A 1 
HETATM 7 O O2A ADP . . . D 2 73.669 122.668 111.402 1 33.75 ? O2A ADP 1844 A 1 
HETATM 8 O O3A ADP . . . D 2 74.592 124.361 109.895 1 34.86 ? O3A ADP 1844 A 1 
HETATM 9 O O5' ADP . . . D 2 74.521 122.109 108.895 1 32.15 ? O5' ADP 1844 A 1 
HETATM 10 C C5' ADP . . . D 2 75.613 121.347 109.356 1 41.13 ? C5' ADP 1844 A 1 
HETATM 11 C C4' ADP . . . D 2 75.766 120.038 108.585 1 44.76 ? C4' ADP 1844 A 1 
HETATM 12 O O4' ADP . . . D 2 74.63 119.252 108.843 1 45.71 ? O4' ADP 1844 A 1 
HETATM 13 C C3' ADP . . . D 2 75.824 120.257 107.096 1 47.24 ? C3' ADP 1844 A 1 
HETATM 14 O O3' ADP . . . D 2 76.81 119.334 106.688 1 50.2 ? O3' ADP 1844 A 1 
HETATM 15 C C2' ADP . . . D 2 74.514 119.794 106.526 1 47.21 ? C2' ADP 1844 A 1 
HETATM 16 O O2' ADP . . . D 2 74.743 119.027 105.331 1 47.34 ? O2' ADP 1844 A 1 
HETATM 17 C C1' ADP . . . D 2 74.002 118.916 107.624 1 48.45 ? C1' ADP 1844 A 1 
HETATM 18 N N9 ADP . . . D 2 72.587 119.092 107.914 1 49.15 ? N9 ADP 1844 A 1 
HETATM 19 C C8 ADP . . . D 2 72 120.161 108.46 1 50.59 ? C8 ADP 1844 A 1 
HETATM 20 N N7 ADP . . . D 2 70.672 119.918 108.617 1 50.98 ? N7 ADP 1844 A 1 
HETATM 21 C C5 ADP . . . D 2 70.436 118.648 108.157 1 51.25 ? C5 ADP 1844 A 1 
HETATM 22 C C6 ADP . . . D 2 69.277 117.717 108.005 1 51.38 ? C6 ADP 1844 A 1 
HETATM 23 N N6 ADP . . . D 2 68.019 118.108 108.4 1 51.73 ? N6 ADP 1844 A 1 
HETATM 24 N N1 ADP . . . D 2 69.496 116.476 107.487 1 49.88 ? N1 ADP 1844 A 1 
HETATM 25 C C2 ADP . . . D 2 70.713 116.076 107.093 1 49.8 ? C2 ADP 1844 A 1 
HETATM 26 N N3 ADP . . . D 2 71.788 116.856 107.207 1 49.88 ? N3 ADP 1844 A 1 
HETATM 27 C C4 ADP . . . D 2 71.717 118.108 107.723 1 49.8 ? C4 ADP 1844 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#