data_2Y3I
#
_model_server_result.job_id            1xrx6W8Q4rZRd8x0sfdVEA 
_model_server_result.datetime_utc      '2024-12-26 14:55:03' 
_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          2y3i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1416}' 
#
_entry.id    2Y3I 
#
_exptl.entry_id    2Y3I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "L-ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            2Y3I 
_cell.length_a            38.419 
_cell.length_b            103.877 
_cell.length_c            203.094 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y3I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,M 1 1 
B,H,I,J,K,L,N 2 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
? 4 E N N 
? 4 H 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 OD1 ASP 375 A ASP 374 1_555 C MG MG . A MG 1416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc2 C MG MG . A MG 1416 1_555 E O3B LA8 . A LA8 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc3 B OD1 ASP 375 D ASP 374 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc4 H O1A LA8 . D LA8 1416 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc5 H O3B LA8 . D LA8 1416 1_555 J MG MG . D MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                LA8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "L-ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     L-ADP 
#
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
C2 N1 LA8 doub 194 n y 
N1 C6 LA8 sing 195 n y 
C2 N3 LA8 sing 196 n y 
C2 H2 LA8 sing 197 n n 
N3 C4 LA8 doub 198 n y 
C4 N9 LA8 sing 199 n y 
C4 C5 LA8 sing 200 n y 
C6 C5 LA8 doub 201 n y 
C5 N7 LA8 sing 202 n y 
C6 N6 LA8 sing 203 n n 
N6 HN6 LA8 sing 204 n n 
N6 HN6A LA8 sing 205 n n 
C8 N7 LA8 doub 206 n y 
N9 C8 LA8 sing 207 n y 
C8 H8 LA8 sing 208 n n 
C1' N9 LA8 sing 209 n n 
O1A PA LA8 doub 210 n n 
PA O5' LA8 sing 211 n n 
PA O3A LA8 sing 212 n n 
PA O2A LA8 sing 213 n n 
O2B PB LA8 doub 214 n n 
O1B PB LA8 sing 215 n n 
PB O3A LA8 sing 216 n n 
PB O3B LA8 sing 217 n n 
C3' C1' LA8 sing 218 n n 
O4' C1' LA8 sing 219 n n 
C1' H1' LA8 sing 220 n n 
O1B HO1B LA8 sing 221 n n 
O2' C2' LA8 sing 222 n n 
C2' C4' LA8 sing 223 n n 
C2' C3' LA8 sing 224 n n 
C2' H2' LA8 sing 225 n n 
O2' HO2' LA8 sing 226 n n 
O2A HO2A LA8 sing 227 n n 
C3' O3' LA8 sing 228 n n 
C3' H3' LA8 sing 229 n n 
O3' HO3' LA8 sing 230 n n 
O3B HO3B LA8 sing 231 n n 
C5' C4' LA8 sing 232 n n 
C4' O4' LA8 sing 233 n n 
C4' H4' LA8 sing 234 n n 
C5' O5' LA8 sing 235 n n 
C5' H5' LA8 sing 236 n n 
C5' "H5'A" LA8 sing 237 n n 
#
_atom_sites.entry_id                     2Y3I 
_atom_sites.fract_transf_matrix[1][1]    0.026029 
_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]    0.009627 
_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]    0.004924 
_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 MG A 1 1416 1416 MG MG . 
D 3 CL A 1 1417 1417 CL CL . 
E 4 LA8 A 1 1418 1418 LA8 LA8 . 
F 5 ALF A 1 1419 1419 ALF ALF . 
G 6 3PG A 1 1420 1420 3PG 3PG . 
H 4 LA8 D 1 1416 1416 LA8 LA8 . 
I 5 ALF D 1 1417 1417 ALF ALF . 
J 2 MG D 1 1418 1418 MG MG . 
K 3 CL D 1 1419 1419 CL CL . 
L 6 3PG D 1 1420 1420 3PG 3PG . 
M 7 HOH A 1 2001 2001 HOH HOH . 
M 7 HOH A 2 2002 2002 HOH HOH . 
M 7 HOH A 3 2003 2003 HOH HOH . 
M 7 HOH A 4 2004 2004 HOH HOH . 
M 7 HOH A 5 2005 2005 HOH HOH . 
M 7 HOH A 6 2006 2006 HOH HOH . 
M 7 HOH A 7 2007 2007 HOH HOH . 
M 7 HOH A 8 2008 2008 HOH HOH . 
N 7 HOH D 1 2001 2001 HOH HOH . 
N 7 HOH D 2 2002 2002 HOH HOH . 
N 7 HOH D 3 2003 2003 HOH HOH . 
N 7 HOH D 4 2004 2004 HOH HOH . 
N 7 HOH D 5 2005 2005 HOH HOH . 
N 7 HOH D 6 2006 2006 HOH HOH . 
N 7 HOH D 7 2007 2007 HOH HOH . 
N 7 HOH D 8 2008 2008 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 N N1 LA8 . . . H 4 -14.627 11.091 -71.694 1 30.44 ? N1 LA8 1416 D 1 
HETATM 2 C C2 LA8 . . . H 4 -15.036 11.754 -70.623 1 30.41 ? C2 LA8 1416 D 1 
HETATM 3 N N3 LA8 . . . H 4 -15.446 11.122 -69.532 1 30.43 ? N3 LA8 1416 D 1 
HETATM 4 C C4 LA8 . . . H 4 -15.465 9.779 -69.475 1 30.61 ? C4 LA8 1416 D 1 
HETATM 5 C C5 LA8 . . . H 4 -15.043 9.054 -70.58 1 30.43 ? C5 LA8 1416 D 1 
HETATM 6 C C6 LA8 . . . H 4 -14.619 9.746 -71.703 1 30.38 ? C6 LA8 1416 D 1 
HETATM 7 N N6 LA8 . . . H 4 -14.211 9.069 -72.767 1 30.43 ? N6 LA8 1416 D 1 
HETATM 8 N N7 LA8 . . . H 4 -15.147 7.76 -70.294 1 30.1 ? N7 LA8 1416 D 1 
HETATM 9 C C8 LA8 . . . H 4 -15.623 7.665 -69.055 1 30.28 ? C8 LA8 1416 D 1 
HETATM 10 N N9 LA8 . . . H 4 -15.817 8.888 -68.544 1 31.14 ? N9 LA8 1416 D 1 
HETATM 11 P PA LA8 . . . H 4 -12.272 9.774 -62.969 1 29.24 ? PA LA8 1416 D 1 
HETATM 12 P PB LA8 . . . H 4 -12.502 8.552 -60.562 1 27.08 ? PB LA8 1416 D 1 
HETATM 13 C C1' LA8 . . . H 4 -16.377 9.161 -67.157 1 32.25 ? C1' LA8 1416 D 1 
HETATM 14 O O1A LA8 . . . H 4 -12.066 10.933 -61.863 1 29.4 ? O1A LA8 1416 D 1 
HETATM 15 O O1B LA8 . . . H 4 -11.022 8.425 -60.01 1 27.24 ? O1B LA8 1416 D 1 
HETATM 16 C C2' LA8 . . . H 4 -15.344 10.784 -65.718 1 33.25 ? C2' LA8 1416 D 1 
HETATM 17 O O2' LA8 . . . H 4 -15.638 11.768 -64.713 1 33.62 ? O2' LA8 1416 D 1 
HETATM 18 O O2A LA8 . . . H 4 -11.143 9.55 -63.914 1 29.55 ? O2A LA8 1416 D 1 
HETATM 19 O O2B LA8 . . . H 4 -13.162 7.238 -60.002 1 27.3 ? O2B LA8 1416 D 1 
HETATM 20 C C3' LA8 . . . H 4 -16.491 10.631 -66.696 1 33.69 ? C3' LA8 1416 D 1 
HETATM 21 O O3' LA8 . . . H 4 -17.73 10.793 -65.983 1 34.8 ? O3' LA8 1416 D 1 
HETATM 22 O O3A LA8 . . . H 4 -12.523 8.434 -62.136 1 27.72 ? O3A LA8 1416 D 1 
HETATM 23 O O3B LA8 . . . H 4 -13.147 9.777 -60.059 1 26.83 ? O3B LA8 1416 D 1 
HETATM 24 C C4' LA8 . . . H 4 -15.431 9.431 -65.077 1 32.45 ? C4' LA8 1416 D 1 
HETATM 25 O O4' LA8 . . . H 4 -15.582 8.517 -66.18 1 32.13 ? O4' LA8 1416 D 1 
HETATM 26 C C5' LA8 . . . H 4 -14.073 9.141 -64.451 1 32.02 ? C5' LA8 1416 D 1 
HETATM 27 O O5' LA8 . . . H 4 -13.566 10.192 -63.701 1 30.38 ? O5' LA8 1416 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#