data_6XK2
#
_model_server_result.job_id            6cvIt-lhQ2Zm8_h1U6hVVQ 
_model_server_result.datetime_utc      '2024-11-27 19:20:55' 
_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          6xk2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":401}' 
#
_entry.id    6XK2 
#
_exptl.entry_id    6XK2 
_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          95.27 
_cell.angle_gamma         90 
_cell.entry_id            6XK2 
_cell.length_a            77.17 
_cell.length_b            84.57 
_cell.length_c            98.27 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XK2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,D,E,F,G,M,N,O,R 1 1 
B,C,H,I,J,K,L,P,Q 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
? 2 E N N 
? 2 H N N 
? 2 K N N 
? 2 M 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 B OE2 GLU 196 B GLU 188 1_555 J NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? 
metalc ? metalc2 M O2A ADP . D ADP 401 1_555 N NA NA . D NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.164 ? 
#
_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                     6XK2 
_atom_sites.fract_transf_matrix[1][1]    0.012958 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001196 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011825 
_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]    0.010219 
_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
E 2 ADP A 1 401 400 ADP ADP . 
F 3 EDO A 1 402 401 EDO EDO . 
G 4 NA A 1 403 405 NA NA . 
H 2 ADP B 1 401 400 ADP ADP . 
I 3 EDO B 1 402 401 EDO EDO . 
J 4 NA B 1 403 405 NA NA . 
K 2 ADP C 1 400 400 ADP ADP . 
L 3 EDO C 1 401 401 EDO EDO . 
M 2 ADP D 1 401 400 ADP ADP . 
N 4 NA D 1 402 405 NA NA . 
O 5 HOH A 1 501 193 HOH HOH . 
O 5 HOH A 2 502 19 HOH HOH . 
O 5 HOH A 3 503 74 HOH HOH . 
O 5 HOH A 4 504 114 HOH HOH . 
O 5 HOH A 5 505 43 HOH HOH . 
O 5 HOH A 6 506 24 HOH HOH . 
O 5 HOH A 7 507 108 HOH HOH . 
O 5 HOH A 8 508 22 HOH HOH . 
O 5 HOH A 9 509 118 HOH HOH . 
O 5 HOH A 10 510 124 HOH HOH . 
O 5 HOH A 11 511 80 HOH HOH . 
O 5 HOH A 12 512 261 HOH HOH . 
O 5 HOH A 13 513 32 HOH HOH . 
O 5 HOH A 14 514 129 HOH HOH . 
O 5 HOH A 15 515 121 HOH HOH . 
O 5 HOH A 16 516 106 HOH HOH . 
O 5 HOH A 17 517 202 HOH HOH . 
O 5 HOH A 18 518 81 HOH HOH . 
O 5 HOH A 19 519 191 HOH HOH . 
O 5 HOH A 20 520 189 HOH HOH . 
O 5 HOH A 21 521 84 HOH HOH . 
O 5 HOH A 22 522 116 HOH HOH . 
O 5 HOH A 23 523 188 HOH HOH . 
O 5 HOH A 24 524 196 HOH HOH . 
O 5 HOH A 25 525 115 HOH HOH . 
O 5 HOH A 26 526 127 HOH HOH . 
O 5 HOH A 27 527 200 HOH HOH . 
O 5 HOH A 28 528 26 HOH HOH . 
O 5 HOH A 29 529 186 HOH HOH . 
O 5 HOH A 30 530 194 HOH HOH . 
O 5 HOH A 31 531 123 HOH HOH . 
O 5 HOH A 32 532 187 HOH HOH . 
O 5 HOH A 33 533 198 HOH HOH . 
O 5 HOH A 34 534 259 HOH HOH . 
O 5 HOH A 35 535 34 HOH HOH . 
O 5 HOH A 36 536 195 HOH HOH . 
O 5 HOH A 37 537 83 HOH HOH . 
O 5 HOH A 38 538 14 HOH HOH . 
O 5 HOH A 39 539 122 HOH HOH . 
O 5 HOH A 40 540 199 HOH HOH . 
O 5 HOH A 41 541 113 HOH HOH . 
O 5 HOH A 42 542 117 HOH HOH . 
O 5 HOH A 43 543 203 HOH HOH . 
O 5 HOH A 44 544 102 HOH HOH . 
O 5 HOH A 45 545 192 HOH HOH . 
O 5 HOH A 46 546 104 HOH HOH . 
O 5 HOH A 47 547 119 HOH HOH . 
O 5 HOH A 48 548 66 HOH HOH . 
O 5 HOH A 49 549 204 HOH HOH . 
O 5 HOH A 50 550 126 HOH HOH . 
O 5 HOH A 51 551 109 HOH HOH . 
O 5 HOH A 52 552 39 HOH HOH . 
O 5 HOH A 53 553 107 HOH HOH . 
O 5 HOH A 54 554 260 HOH HOH . 
O 5 HOH A 55 555 103 HOH HOH . 
O 5 HOH A 56 556 63 HOH HOH . 
O 5 HOH A 57 557 185 HOH HOH . 
P 5 HOH B 1 501 143 HOH HOH . 
P 5 HOH B 2 502 147 HOH HOH . 
P 5 HOH B 3 503 216 HOH HOH . 
P 5 HOH B 4 504 154 HOH HOH . 
P 5 HOH B 5 505 263 HOH HOH . 
P 5 HOH B 6 506 208 HOH HOH . 
P 5 HOH B 7 507 12 HOH HOH . 
P 5 HOH B 8 508 220 HOH HOH . 
P 5 HOH B 9 509 137 HOH HOH . 
P 5 HOH B 10 510 23 HOH HOH . 
P 5 HOH B 11 511 150 HOH HOH . 
P 5 HOH B 12 512 153 HOH HOH . 
P 5 HOH B 13 513 18 HOH HOH . 
P 5 HOH B 14 514 135 HOH HOH . 
P 5 HOH B 15 515 30 HOH HOH . 
P 5 HOH B 16 516 131 HOH HOH . 
P 5 HOH B 17 517 264 HOH HOH . 
P 5 HOH B 18 518 90 HOH HOH . 
P 5 HOH B 19 519 7 HOH HOH . 
P 5 HOH B 20 520 144 HOH HOH . 
P 5 HOH B 21 521 27 HOH HOH . 
P 5 HOH B 22 522 136 HOH HOH . 
P 5 HOH B 23 523 146 HOH HOH . 
P 5 HOH B 24 524 132 HOH HOH . 
P 5 HOH B 25 525 5 HOH HOH . 
P 5 HOH B 26 526 86 HOH HOH . 
P 5 HOH B 27 527 211 HOH HOH . 
P 5 HOH B 28 528 139 HOH HOH . 
P 5 HOH B 29 529 13 HOH HOH . 
P 5 HOH B 30 530 213 HOH HOH . 
P 5 HOH B 31 531 88 HOH HOH . 
P 5 HOH B 32 532 215 HOH HOH . 
P 5 HOH B 33 533 152 HOH HOH . 
P 5 HOH B 34 534 36 HOH HOH . 
P 5 HOH B 35 535 210 HOH HOH . 
P 5 HOH B 36 536 89 HOH HOH . 
P 5 HOH B 37 537 141 HOH HOH . 
P 5 HOH B 38 538 15 HOH HOH . 
P 5 HOH B 39 539 45 HOH HOH . 
P 5 HOH B 40 540 101 HOH HOH . 
P 5 HOH B 41 541 219 HOH HOH . 
P 5 HOH B 42 542 40 HOH HOH . 
P 5 HOH B 43 543 151 HOH HOH . 
P 5 HOH B 44 544 134 HOH HOH . 
P 5 HOH B 45 545 212 HOH HOH . 
P 5 HOH B 46 546 262 HOH HOH . 
P 5 HOH B 47 547 52 HOH HOH . 
P 5 HOH B 48 548 149 HOH HOH . 
P 5 HOH B 49 549 217 HOH HOH . 
P 5 HOH B 50 550 218 HOH HOH . 
P 5 HOH B 51 551 201 HOH HOH . 
P 5 HOH B 52 552 206 HOH HOH . 
P 5 HOH B 53 553 145 HOH HOH . 
P 5 HOH B 54 554 87 HOH HOH . 
P 5 HOH B 55 555 207 HOH HOH . 
Q 5 HOH C 1 501 158 HOH HOH . 
Q 5 HOH C 2 502 165 HOH HOH . 
Q 5 HOH C 3 503 163 HOH HOH . 
Q 5 HOH C 4 504 268 HOH HOH . 
Q 5 HOH C 5 505 231 HOH HOH . 
Q 5 HOH C 6 506 230 HOH HOH . 
Q 5 HOH C 7 507 98 HOH HOH . 
Q 5 HOH C 8 508 224 HOH HOH . 
Q 5 HOH C 9 509 232 HOH HOH . 
Q 5 HOH C 10 510 155 HOH HOH . 
Q 5 HOH C 11 511 50 HOH HOH . 
Q 5 HOH C 12 512 164 HOH HOH . 
Q 5 HOH C 13 513 76 HOH HOH . 
Q 5 HOH C 14 514 91 HOH HOH . 
Q 5 HOH C 15 515 241 HOH HOH . 
Q 5 HOH C 16 516 156 HOH HOH . 
Q 5 HOH C 17 517 225 HOH HOH . 
Q 5 HOH C 18 518 222 HOH HOH . 
Q 5 HOH C 19 519 238 HOH HOH . 
Q 5 HOH C 20 520 97 HOH HOH . 
Q 5 HOH C 21 521 161 HOH HOH . 
Q 5 HOH C 22 522 235 HOH HOH . 
Q 5 HOH C 23 523 96 HOH HOH . 
Q 5 HOH C 24 524 41 HOH HOH . 
Q 5 HOH C 25 525 239 HOH HOH . 
Q 5 HOH C 26 526 227 HOH HOH . 
Q 5 HOH C 27 527 160 HOH HOH . 
Q 5 HOH C 28 528 258 HOH HOH . 
Q 5 HOH C 29 529 223 HOH HOH . 
R 5 HOH D 1 501 257 HOH HOH . 
R 5 HOH D 2 502 247 HOH HOH . 
R 5 HOH D 3 503 111 HOH HOH . 
R 5 HOH D 4 504 133 HOH HOH . 
R 5 HOH D 5 505 178 HOH HOH . 
R 5 HOH D 6 506 175 HOH HOH . 
R 5 HOH D 7 507 180 HOH HOH . 
R 5 HOH D 8 508 171 HOH HOH . 
R 5 HOH D 9 509 172 HOH HOH . 
R 5 HOH D 10 510 176 HOH HOH . 
R 5 HOH D 11 511 174 HOH HOH . 
R 5 HOH D 12 512 182 HOH HOH . 
R 5 HOH D 13 513 173 HOH HOH . 
R 5 HOH D 14 514 159 HOH HOH . 
R 5 HOH D 15 515 250 HOH HOH . 
R 5 HOH D 16 516 169 HOH HOH . 
R 5 HOH D 17 517 181 HOH HOH . 
R 5 HOH D 18 518 252 HOH HOH . 
R 5 HOH D 19 519 243 HOH HOH . 
R 5 HOH D 20 520 255 HOH HOH . 
R 5 HOH D 21 521 100 HOH HOH . 
R 5 HOH D 22 522 170 HOH HOH . 
R 5 HOH D 23 523 267 HOH HOH . 
R 5 HOH D 24 524 244 HOH HOH . 
R 5 HOH D 25 525 177 HOH HOH . 
R 5 HOH D 26 526 246 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 . . . M 2 21.671 -18.753 -52.206 0.87 71.01 ? PB ADP 401 D 1 
HETATM 2 O O1B ADP . . . M 2 21.426 -17.234 -52.45 0.87 68.81 ? O1B ADP 401 D 1 
HETATM 3 O O2B ADP . . . M 2 20.347 -19.355 -51.625 0.87 65.37 ? O2B ADP 401 D 1 
HETATM 4 O O3B ADP . . . M 2 22.91 -19.067 -51.375 0.87 61.83 ? O3B ADP 401 D 1 
HETATM 5 P PA ADP . . . M 2 21.659 -18.716 -55.085 0.87 55.32 ? PA ADP 401 D 1 
HETATM 6 O O1A ADP . . . M 2 22.944 -17.937 -55.412 0.87 60.71 ? O1A ADP 401 D 1 
HETATM 7 O O2A ADP . . . M 2 20.532 -17.754 -55.041 0.87 62.09 ? O2A ADP 401 D 1 
HETATM 8 O O3A ADP . . . M 2 21.85 -19.387 -53.656 0.87 59.31 ? O3A ADP 401 D 1 
HETATM 9 O O5' ADP . . . M 2 21.565 -19.953 -56.077 0.87 55.93 ? O5' ADP 401 D 1 
HETATM 10 C C5' ADP . . . M 2 22.598 -20.954 -56.198 0.87 54.14 ? C5' ADP 401 D 1 
HETATM 11 C C4' ADP . . . M 2 22.653 -21.387 -57.64 0.87 55.33 ? C4' ADP 401 D 1 
HETATM 12 O O4' ADP . . . M 2 21.352 -21.849 -58.061 0.87 56.27 ? O4' ADP 401 D 1 
HETATM 13 C C3' ADP . . . M 2 22.988 -20.273 -58.622 0.87 55.4 ? C3' ADP 401 D 1 
HETATM 14 O O3' ADP . . . M 2 24.385 -20.011 -58.686 0.87 56.01 ? O3' ADP 401 D 1 
HETATM 15 C C2' ADP . . . M 2 22.391 -20.816 -59.92 0.87 54.41 ? C2' ADP 401 D 1 
HETATM 16 O O2' ADP . . . M 2 23.151 -21.844 -60.537 0.87 54.58 ? O2' ADP 401 D 1 
HETATM 17 C C1' ADP . . . M 2 21.104 -21.453 -59.4 0.87 56.44 ? C1' ADP 401 D 1 
HETATM 18 N N9 ADP . . . M 2 19.974 -20.54 -59.428 0.87 55.74 ? N9 ADP 401 D 1 
HETATM 19 C C8 ADP . . . M 2 19.456 -19.803 -58.389 0.87 55.59 ? C8 ADP 401 D 1 
HETATM 20 N N7 ADP . . . M 2 18.506 -18.979 -58.739 0.87 56.48 ? N7 ADP 401 D 1 
HETATM 21 C C5 ADP . . . M 2 18.372 -19.185 -60.114 0.87 58.72 ? C5 ADP 401 D 1 
HETATM 22 C C6 ADP . . . M 2 17.548 -18.6 -61.081 0.87 59.08 ? C6 ADP 401 D 1 
HETATM 23 N N6 ADP . . . M 2 16.658 -17.637 -60.823 0.87 55.69 ? N6 ADP 401 D 1 
HETATM 24 N N1 ADP . . . M 2 17.685 -19.024 -62.359 0.87 57.87 ? N1 ADP 401 D 1 
HETATM 25 C C2 ADP . . . M 2 18.592 -19.97 -62.629 0.87 58.29 ? C2 ADP 401 D 1 
HETATM 26 N N3 ADP . . . M 2 19.428 -20.593 -61.797 0.87 56.7 ? N3 ADP 401 D 1 
HETATM 27 C C4 ADP . . . M 2 19.272 -20.151 -60.533 0.87 57.25 ? C4 ADP 401 D 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#