data_5KB5
#
_model_server_result.job_id            k7TAVWckLth0G5KeRI0yhA 
_model_server_result.datetime_utc      '2024-11-23 13:45:44' 
_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          5kb5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    5KB5 
#
_exptl.entry_id    5KB5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            5KB5 
_cell.length_a            49.264 
_cell.length_b            73.559 
_cell.length_c            84.33 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KB5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 O ASP 312 A ASP 310 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
metalc ? metalc2 A OD1 ASP 312 A ASP 310 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc3 A O ASN 314 A ASN 312 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? 
metalc ? metalc4 A O ILE 348 A ILE 346 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc5 A O ARG 351 A ARG 349 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc6 A O GLY 353 A GLY 351 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc7 C O2B ADP . A ADP 402 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc8 C O1A ADP . A ADP 402 1_555 G MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc9 F MG MG . A MG 405 1_555 L O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc10 F MG MG . A MG 405 1_555 L O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc11 F MG MG . A MG 405 1_555 L O HOH . A HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc12 F MG MG . A MG 405 1_555 L O HOH . A HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc13 G MG MG . A MG 406 1_555 L O HOH . A HOH 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? 
metalc ? metalc14 G MG MG . A MG 406 1_555 L O HOH . A HOH 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc15 G MG MG . A MG 406 1_555 L O HOH . A HOH 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc16 G MG MG . A MG 406 1_555 L O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
#
_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 35 n n 
PB O2B ADP sing 36 n n 
PB O3B ADP sing 37 n n 
PB O3A ADP sing 38 n n 
O2B HOB2 ADP sing 39 n n 
O3B HOB3 ADP sing 40 n n 
PA O1A ADP doub 41 n n 
PA O2A ADP sing 42 n n 
PA O3A ADP sing 43 n n 
PA O5' ADP sing 44 n n 
O2A HOA2 ADP sing 45 n n 
O5' C5' ADP sing 46 n n 
C5' C4' ADP sing 47 n n 
C5' "H5'1" ADP sing 48 n n 
C5' "H5'2" ADP sing 49 n n 
C4' O4' ADP sing 50 n n 
C4' C3' ADP sing 51 n n 
C4' H4' ADP sing 52 n n 
O4' C1' ADP sing 53 n n 
C3' O3' ADP sing 54 n n 
C3' C2' ADP sing 55 n n 
C3' H3' ADP sing 56 n n 
O3' HO3' ADP sing 57 n n 
C2' O2' ADP sing 58 n n 
C2' C1' ADP sing 59 n n 
C2' H2' ADP sing 60 n n 
O2' HO2' ADP sing 61 n n 
C1' N9 ADP sing 62 n n 
C1' H1' ADP sing 63 n n 
N9 C8 ADP sing 64 n y 
N9 C4 ADP sing 65 n y 
C8 N7 ADP doub 66 n y 
C8 H8 ADP sing 67 n n 
N7 C5 ADP sing 68 n y 
C5 C6 ADP sing 69 n y 
C5 C4 ADP doub 70 n y 
C6 N6 ADP sing 71 n n 
C6 N1 ADP doub 72 n y 
N6 HN61 ADP sing 73 n n 
N6 HN62 ADP sing 74 n n 
N1 C2 ADP sing 75 n y 
C2 N3 ADP doub 76 n y 
C2 H2 ADP sing 77 n n 
N3 C4 ADP sing 78 n y 
#
_atom_sites.entry_id                     5KB5 
_atom_sites.fract_transf_matrix[1][1]    0.020299 
_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]    0.013595 
_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]    0.011858 
_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
B 2 ADN A 1 401 1 ADN ADN . 
C 3 ADP A 1 402 1 ADP ADP . 
D 4 K A 1 403 1 K K . 
E 5 CL A 1 404 1 CL CL . 
F 6 MG A 1 405 1 MG MG . 
G 6 MG A 1 406 2 MG MG . 
H 7 PG4 A 1 407 1 PG4 PG4 . 
I 7 PG4 A 1 408 2 PG4 PG4 . 
J 8 PO4 A 1 409 1 PO4 PO4 . 
K 8 PO4 A 1 410 2 PO4 PO4 . 
L 9 HOH A 1 501 101 HOH HOH . 
L 9 HOH A 2 502 85 HOH HOH . 
L 9 HOH A 3 503 49 HOH HOH . 
L 9 HOH A 4 504 35 HOH HOH . 
L 9 HOH A 5 505 64 HOH HOH . 
L 9 HOH A 6 506 150 HOH HOH . 
L 9 HOH A 7 507 24 HOH HOH . 
L 9 HOH A 8 508 106 HOH HOH . 
L 9 HOH A 9 509 43 HOH HOH . 
L 9 HOH A 10 510 113 HOH HOH . 
L 9 HOH A 11 511 10 HOH HOH . 
L 9 HOH A 12 512 142 HOH HOH . 
L 9 HOH A 13 513 20 HOH HOH . 
L 9 HOH A 14 514 33 HOH HOH . 
L 9 HOH A 15 515 44 HOH HOH . 
L 9 HOH A 16 516 18 HOH HOH . 
L 9 HOH A 17 517 74 HOH HOH . 
L 9 HOH A 18 518 25 HOH HOH . 
L 9 HOH A 19 519 11 HOH HOH . 
L 9 HOH A 20 520 3 HOH HOH . 
L 9 HOH A 21 521 9 HOH HOH . 
L 9 HOH A 22 522 31 HOH HOH . 
L 9 HOH A 23 523 81 HOH HOH . 
L 9 HOH A 24 524 32 HOH HOH . 
L 9 HOH A 25 525 28 HOH HOH . 
L 9 HOH A 26 526 2 HOH HOH . 
L 9 HOH A 27 527 19 HOH HOH . 
L 9 HOH A 28 528 46 HOH HOH . 
L 9 HOH A 29 529 14 HOH HOH . 
L 9 HOH A 30 530 97 HOH HOH . 
L 9 HOH A 31 531 6 HOH HOH . 
L 9 HOH A 32 532 181 HOH HOH . 
L 9 HOH A 33 533 59 HOH HOH . 
L 9 HOH A 34 534 63 HOH HOH . 
L 9 HOH A 35 535 1 HOH HOH . 
L 9 HOH A 36 536 65 HOH HOH . 
L 9 HOH A 37 537 41 HOH HOH . 
L 9 HOH A 38 538 69 HOH HOH . 
L 9 HOH A 39 539 110 HOH HOH . 
L 9 HOH A 40 540 179 HOH HOH . 
L 9 HOH A 41 541 80 HOH HOH . 
L 9 HOH A 42 542 54 HOH HOH . 
L 9 HOH A 43 543 70 HOH HOH . 
L 9 HOH A 44 544 38 HOH HOH . 
L 9 HOH A 45 545 7 HOH HOH . 
L 9 HOH A 46 546 173 HOH HOH . 
L 9 HOH A 47 547 55 HOH HOH . 
L 9 HOH A 48 548 168 HOH HOH . 
L 9 HOH A 49 549 61 HOH HOH . 
L 9 HOH A 50 550 29 HOH HOH . 
L 9 HOH A 51 551 50 HOH HOH . 
L 9 HOH A 52 552 17 HOH HOH . 
L 9 HOH A 53 553 42 HOH HOH . 
L 9 HOH A 54 554 40 HOH HOH . 
L 9 HOH A 55 555 84 HOH HOH . 
L 9 HOH A 56 556 72 HOH HOH . 
L 9 HOH A 57 557 88 HOH HOH . 
L 9 HOH A 58 558 147 HOH HOH . 
L 9 HOH A 59 559 124 HOH HOH . 
L 9 HOH A 60 560 158 HOH HOH . 
L 9 HOH A 61 561 26 HOH HOH . 
L 9 HOH A 62 562 34 HOH HOH . 
L 9 HOH A 63 563 172 HOH HOH . 
L 9 HOH A 64 564 21 HOH HOH . 
L 9 HOH A 65 565 132 HOH HOH . 
L 9 HOH A 66 566 48 HOH HOH . 
L 9 HOH A 67 567 5 HOH HOH . 
L 9 HOH A 68 568 157 HOH HOH . 
L 9 HOH A 69 569 73 HOH HOH . 
L 9 HOH A 70 570 16 HOH HOH . 
L 9 HOH A 71 571 90 HOH HOH . 
L 9 HOH A 72 572 57 HOH HOH . 
L 9 HOH A 73 573 47 HOH HOH . 
L 9 HOH A 74 574 98 HOH HOH . 
L 9 HOH A 75 575 12 HOH HOH . 
L 9 HOH A 76 576 122 HOH HOH . 
L 9 HOH A 77 577 100 HOH HOH . 
L 9 HOH A 78 578 152 HOH HOH . 
L 9 HOH A 79 579 13 HOH HOH . 
L 9 HOH A 80 580 169 HOH HOH . 
L 9 HOH A 81 581 92 HOH HOH . 
L 9 HOH A 82 582 134 HOH HOH . 
L 9 HOH A 83 583 94 HOH HOH . 
L 9 HOH A 84 584 91 HOH HOH . 
L 9 HOH A 85 585 8 HOH HOH . 
L 9 HOH A 86 586 175 HOH HOH . 
L 9 HOH A 87 587 79 HOH HOH . 
L 9 HOH A 88 588 112 HOH HOH . 
L 9 HOH A 89 589 83 HOH HOH . 
L 9 HOH A 90 590 127 HOH HOH . 
L 9 HOH A 91 591 143 HOH HOH . 
L 9 HOH A 92 592 62 HOH HOH . 
L 9 HOH A 93 593 123 HOH HOH . 
L 9 HOH A 94 594 78 HOH HOH . 
L 9 HOH A 95 595 66 HOH HOH . 
L 9 HOH A 96 596 60 HOH HOH . 
L 9 HOH A 97 597 22 HOH HOH . 
L 9 HOH A 98 598 76 HOH HOH . 
L 9 HOH A 99 599 53 HOH HOH . 
L 9 HOH A 100 600 136 HOH HOH . 
L 9 HOH A 101 601 170 HOH HOH . 
L 9 HOH A 102 602 135 HOH HOH . 
L 9 HOH A 103 603 153 HOH HOH . 
L 9 HOH A 104 604 51 HOH HOH . 
L 9 HOH A 105 605 99 HOH HOH . 
L 9 HOH A 106 606 107 HOH HOH . 
L 9 HOH A 107 607 144 HOH HOH . 
L 9 HOH A 108 608 37 HOH HOH . 
L 9 HOH A 109 609 176 HOH HOH . 
L 9 HOH A 110 610 137 HOH HOH . 
L 9 HOH A 111 611 129 HOH HOH . 
L 9 HOH A 112 612 82 HOH HOH . 
L 9 HOH A 113 613 58 HOH HOH . 
L 9 HOH A 114 614 75 HOH HOH . 
L 9 HOH A 115 615 118 HOH HOH . 
L 9 HOH A 116 616 130 HOH HOH . 
L 9 HOH A 117 617 178 HOH HOH . 
L 9 HOH A 118 618 177 HOH HOH . 
L 9 HOH A 119 619 27 HOH HOH . 
L 9 HOH A 120 620 30 HOH HOH . 
L 9 HOH A 121 621 52 HOH HOH . 
L 9 HOH A 122 622 15 HOH HOH . 
L 9 HOH A 123 623 138 HOH HOH . 
L 9 HOH A 124 624 56 HOH HOH . 
L 9 HOH A 125 625 111 HOH HOH . 
L 9 HOH A 126 626 149 HOH HOH . 
L 9 HOH A 127 627 140 HOH HOH . 
L 9 HOH A 128 628 71 HOH HOH . 
L 9 HOH A 129 629 174 HOH HOH . 
L 9 HOH A 130 630 45 HOH HOH . 
L 9 HOH A 131 631 87 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 . . . C 3 164.278 156.594 183.815 1 18.37 ? PB ADP 402 A 1 
HETATM 2 O O1B ADP . . . C 3 164.822 157.591 182.832 1 19.37 ? O1B ADP 402 A 1 
HETATM 3 O O2B ADP . . . C 3 163.729 157.259 185.057 1 18.88 ? O2B ADP 402 A 1 
HETATM 4 O O3B ADP . . . C 3 163.317 155.548 183.257 1 17.76 ? O3B ADP 402 A 1 
HETATM 5 P PA ADP . . . C 3 166.878 155.122 183.937 1 17.4 ? PA ADP 402 A 1 
HETATM 6 O O1A ADP . . . C 3 167.05 155.208 182.435 1 16.59 ? O1A ADP 402 A 1 
HETATM 7 O O2A ADP . . . C 3 167.974 155.702 184.775 1 15.28 ? O2A ADP 402 A 1 
HETATM 8 O O3A ADP . . . C 3 165.496 155.777 184.485 1 16.54 ? O3A ADP 402 A 1 
HETATM 9 O O5' ADP . . . C 3 166.635 153.611 184.194 1 15.6 ? O5' ADP 402 A 1 
HETATM 10 C C5' ADP . . . C 3 166.372 153.11 185.512 1 14.19 ? C5' ADP 402 A 1 
HETATM 11 C C4' ADP . . . C 3 166.904 151.703 185.678 1 14.71 ? C4' ADP 402 A 1 
HETATM 12 O O4' ADP . . . C 3 166.495 150.839 184.595 1 14.17 ? O4' ADP 402 A 1 
HETATM 13 C C3' ADP . . . C 3 168.429 151.584 185.685 1 15.23 ? C3' ADP 402 A 1 
HETATM 14 O O3' ADP . . . C 3 169.004 151.891 186.941 1 16.08 ? O3' ADP 402 A 1 
HETATM 15 C C2' ADP . . . C 3 168.636 150.148 185.3 1 15.26 ? C2' ADP 402 A 1 
HETATM 16 O O2' ADP . . . C 3 168.376 149.321 186.437 1 15.28 ? O2' ADP 402 A 1 
HETATM 17 C C1' ADP . . . C 3 167.543 149.944 184.244 1 14.84 ? C1' ADP 402 A 1 
HETATM 18 N N9 ADP . . . C 3 167.967 150.31 182.876 1 16.42 ? N9 ADP 402 A 1 
HETATM 19 C C8 ADP . . . C 3 167.554 151.368 182.128 1 17.35 ? C8 ADP 402 A 1 
HETATM 20 N N7 ADP . . . C 3 168.165 151.402 180.911 1 17.57 ? N7 ADP 402 A 1 
HETATM 21 C C5 ADP . . . C 3 168.955 150.312 180.898 1 19.24 ? C5 ADP 402 A 1 
HETATM 22 C C6 ADP . . . C 3 169.886 149.737 179.943 1 22.02 ? C6 ADP 402 A 1 
HETATM 23 N N6 ADP . . . C 3 170.023 150.355 178.731 1 22.56 ? N6 ADP 402 A 1 
HETATM 24 N N1 ADP . . . C 3 170.55 148.629 180.288 1 22.41 ? N1 ADP 402 A 1 
HETATM 25 C C2 ADP . . . C 3 170.389 148.001 181.466 1 22.83 ? C2 ADP 402 A 1 
HETATM 26 N N3 ADP . . . C 3 169.553 148.486 182.403 1 20.27 ? N3 ADP 402 A 1 
HETATM 27 C C4 ADP . . . C 3 168.834 149.604 182.169 1 18.27 ? C4 ADP 402 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#