data_4NYE
#
_model_server_result.job_id            Vju9r_kZCfm7U41GLh6zQA 
_model_server_result.datetime_utc      '2025-06-18 09:21:08' 
_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          4nye 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    4NYE 
#
_exptl.entry_id    4NYE 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.96 
_cell.angle_gamma         90 
_cell.entry_id            4NYE 
_cell.length_a            45.931 
_cell.length_b            65.111 
_cell.length_c            85.837 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NYE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 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 C MG MG . A MG 301 1_555 D O3B ADP . A ADP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc2 C MG MG . A MG 301 1_555 D O2A ADP . A ADP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc3 C MG MG . A MG 301 1_555 J O HOH . A HOH 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? 
metalc ? metalc4 G MG MG . B MG 301 1_555 H O3B ADP . B ADP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc5 G MG MG . B MG 301 1_555 H O2A ADP . B ADP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? 
metalc ? metalc6 G MG MG . B MG 301 1_555 K O HOH . B HOH 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
#
_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 7 n n 
PB O2B ADP sing 8 n n 
PB O3B ADP sing 9 n n 
PB O3A ADP sing 10 n n 
O2B HOB2 ADP sing 11 n n 
O3B HOB3 ADP sing 12 n n 
PA O1A ADP doub 13 n n 
PA O2A ADP sing 14 n n 
PA O3A ADP sing 15 n n 
PA O5' ADP sing 16 n n 
O2A HOA2 ADP sing 17 n n 
O5' C5' ADP sing 18 n n 
C5' C4' ADP sing 19 n n 
C5' "H5'1" ADP sing 20 n n 
C5' "H5'2" ADP sing 21 n n 
C4' O4' ADP sing 22 n n 
C4' C3' ADP sing 23 n n 
C4' H4' ADP sing 24 n n 
O4' C1' ADP sing 25 n n 
C3' O3' ADP sing 26 n n 
C3' C2' ADP sing 27 n n 
C3' H3' ADP sing 28 n n 
O3' HO3' ADP sing 29 n n 
C2' O2' ADP sing 30 n n 
C2' C1' ADP sing 31 n n 
C2' H2' ADP sing 32 n n 
O2' HO2' ADP sing 33 n n 
C1' N9 ADP sing 34 n n 
C1' H1' ADP sing 35 n n 
N9 C8 ADP sing 36 n y 
N9 C4 ADP sing 37 n y 
C8 N7 ADP doub 38 n y 
C8 H8 ADP sing 39 n n 
N7 C5 ADP sing 40 n y 
C5 C6 ADP sing 41 n y 
C5 C4 ADP doub 42 n y 
C6 N6 ADP sing 43 n n 
C6 N1 ADP doub 44 n y 
N6 HN61 ADP sing 45 n n 
N6 HN62 ADP sing 46 n n 
N1 C2 ADP sing 47 n y 
C2 N3 ADP doub 48 n y 
C2 H2 ADP sing 49 n n 
N3 C4 ADP sing 50 n y 
#
_atom_sites.entry_id                     4NYE 
_atom_sites.fract_transf_matrix[1][1]    0.021772 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000745 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015358 
_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]    0.011657 
_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 1 301 301 MG MG . 
D 3 ADP A 1 302 302 ADP ADP . 
E 4 CL A 1 303 303 CL CL . 
F 5 ACT A 1 304 304 ACT ACT . 
G 2 MG B 1 301 301 MG MG . 
H 3 ADP B 1 302 302 ADP ADP . 
I 5 ACT B 1 303 303 ACT ACT . 
J 6 HOH A 1 401 401 HOH HOH . 
J 6 HOH A 2 402 402 HOH HOH . 
J 6 HOH A 3 403 403 HOH HOH . 
J 6 HOH A 4 404 404 HOH HOH . 
J 6 HOH A 5 405 405 HOH HOH . 
J 6 HOH A 6 406 406 HOH HOH . 
J 6 HOH A 7 407 407 HOH HOH . 
J 6 HOH A 8 408 408 HOH HOH . 
J 6 HOH A 9 409 409 HOH HOH . 
J 6 HOH A 10 410 410 HOH HOH . 
J 6 HOH A 11 411 411 HOH HOH . 
J 6 HOH A 12 412 412 HOH HOH . 
J 6 HOH A 13 413 413 HOH HOH . 
J 6 HOH A 14 414 414 HOH HOH . 
J 6 HOH A 15 415 415 HOH HOH . 
J 6 HOH A 16 416 416 HOH HOH . 
J 6 HOH A 17 417 417 HOH HOH . 
J 6 HOH A 18 418 418 HOH HOH . 
J 6 HOH A 19 419 419 HOH HOH . 
J 6 HOH A 20 420 420 HOH HOH . 
J 6 HOH A 21 421 421 HOH HOH . 
J 6 HOH A 22 422 422 HOH HOH . 
J 6 HOH A 23 423 423 HOH HOH . 
J 6 HOH A 24 424 424 HOH HOH . 
J 6 HOH A 25 425 425 HOH HOH . 
J 6 HOH A 26 426 426 HOH HOH . 
J 6 HOH A 27 427 427 HOH HOH . 
J 6 HOH A 28 428 428 HOH HOH . 
J 6 HOH A 29 429 429 HOH HOH . 
J 6 HOH A 30 430 430 HOH HOH . 
J 6 HOH A 31 431 431 HOH HOH . 
J 6 HOH A 32 432 432 HOH HOH . 
J 6 HOH A 33 433 433 HOH HOH . 
J 6 HOH A 34 434 434 HOH HOH . 
J 6 HOH A 35 435 435 HOH HOH . 
J 6 HOH A 36 436 436 HOH HOH . 
J 6 HOH A 37 437 437 HOH HOH . 
J 6 HOH A 38 438 438 HOH HOH . 
J 6 HOH A 39 439 439 HOH HOH . 
J 6 HOH A 40 440 440 HOH HOH . 
J 6 HOH A 41 441 441 HOH HOH . 
J 6 HOH A 42 442 442 HOH HOH . 
J 6 HOH A 43 443 443 HOH HOH . 
J 6 HOH A 44 444 444 HOH HOH . 
J 6 HOH A 45 445 445 HOH HOH . 
J 6 HOH A 46 446 446 HOH HOH . 
J 6 HOH A 47 447 447 HOH HOH . 
J 6 HOH A 48 448 448 HOH HOH . 
J 6 HOH A 49 449 449 HOH HOH . 
J 6 HOH A 50 450 450 HOH HOH . 
J 6 HOH A 51 451 451 HOH HOH . 
J 6 HOH A 52 452 452 HOH HOH . 
J 6 HOH A 53 453 453 HOH HOH . 
J 6 HOH A 54 454 454 HOH HOH . 
J 6 HOH A 55 455 455 HOH HOH . 
J 6 HOH A 56 456 456 HOH HOH . 
J 6 HOH A 57 457 457 HOH HOH . 
J 6 HOH A 58 458 458 HOH HOH . 
J 6 HOH A 59 459 459 HOH HOH . 
J 6 HOH A 60 460 460 HOH HOH . 
J 6 HOH A 61 461 461 HOH HOH . 
J 6 HOH A 62 462 462 HOH HOH . 
J 6 HOH A 63 463 463 HOH HOH . 
J 6 HOH A 64 464 464 HOH HOH . 
J 6 HOH A 65 465 465 HOH HOH . 
J 6 HOH A 66 466 466 HOH HOH . 
J 6 HOH A 67 467 467 HOH HOH . 
J 6 HOH A 68 468 468 HOH HOH . 
J 6 HOH A 69 469 469 HOH HOH . 
J 6 HOH A 70 470 470 HOH HOH . 
J 6 HOH A 71 471 471 HOH HOH . 
J 6 HOH A 72 472 472 HOH HOH . 
J 6 HOH A 73 473 473 HOH HOH . 
J 6 HOH A 74 474 474 HOH HOH . 
J 6 HOH A 75 475 475 HOH HOH . 
J 6 HOH A 76 476 476 HOH HOH . 
J 6 HOH A 77 477 477 HOH HOH . 
J 6 HOH A 78 478 478 HOH HOH . 
J 6 HOH A 79 479 479 HOH HOH . 
J 6 HOH A 80 480 480 HOH HOH . 
J 6 HOH A 81 481 481 HOH HOH . 
J 6 HOH A 82 482 482 HOH HOH . 
J 6 HOH A 83 483 483 HOH HOH . 
J 6 HOH A 84 484 484 HOH HOH . 
J 6 HOH A 85 485 485 HOH HOH . 
J 6 HOH A 86 486 486 HOH HOH . 
K 6 HOH B 1 401 401 HOH HOH . 
K 6 HOH B 2 402 402 HOH HOH . 
K 6 HOH B 3 403 403 HOH HOH . 
K 6 HOH B 4 404 404 HOH HOH . 
K 6 HOH B 5 405 405 HOH HOH . 
K 6 HOH B 6 406 406 HOH HOH . 
K 6 HOH B 7 407 407 HOH HOH . 
K 6 HOH B 8 408 408 HOH HOH . 
K 6 HOH B 9 409 409 HOH HOH . 
K 6 HOH B 10 410 410 HOH HOH . 
K 6 HOH B 11 411 411 HOH HOH . 
K 6 HOH B 12 412 412 HOH HOH . 
K 6 HOH B 13 413 413 HOH HOH . 
K 6 HOH B 14 414 414 HOH HOH . 
K 6 HOH B 15 415 415 HOH HOH . 
K 6 HOH B 16 416 416 HOH HOH . 
K 6 HOH B 17 417 417 HOH HOH . 
K 6 HOH B 18 418 418 HOH HOH . 
K 6 HOH B 19 419 419 HOH HOH . 
K 6 HOH B 20 420 420 HOH HOH . 
K 6 HOH B 21 421 421 HOH HOH . 
K 6 HOH B 22 422 422 HOH HOH . 
K 6 HOH B 23 423 423 HOH HOH . 
K 6 HOH B 24 424 424 HOH HOH . 
K 6 HOH B 25 425 425 HOH HOH . 
K 6 HOH B 26 426 426 HOH HOH . 
K 6 HOH B 27 427 427 HOH HOH . 
K 6 HOH B 28 428 428 HOH HOH . 
K 6 HOH B 29 429 429 HOH HOH . 
K 6 HOH B 30 430 430 HOH HOH . 
K 6 HOH B 31 431 431 HOH HOH . 
K 6 HOH B 32 432 432 HOH HOH . 
K 6 HOH B 33 433 433 HOH HOH . 
K 6 HOH B 34 434 434 HOH HOH . 
K 6 HOH B 35 435 435 HOH HOH . 
K 6 HOH B 36 436 436 HOH HOH . 
K 6 HOH B 37 437 437 HOH HOH . 
K 6 HOH B 38 438 438 HOH HOH . 
K 6 HOH B 39 439 439 HOH HOH . 
K 6 HOH B 40 440 440 HOH HOH . 
K 6 HOH B 41 441 441 HOH HOH . 
K 6 HOH B 42 442 442 HOH HOH . 
K 6 HOH B 43 443 443 HOH HOH . 
K 6 HOH B 44 444 444 HOH HOH . 
K 6 HOH B 45 445 445 HOH HOH . 
K 6 HOH B 46 446 446 HOH HOH . 
K 6 HOH B 47 447 447 HOH HOH . 
K 6 HOH B 48 448 448 HOH HOH . 
K 6 HOH B 49 449 449 HOH HOH . 
K 6 HOH B 50 450 450 HOH HOH . 
K 6 HOH B 51 451 451 HOH HOH . 
K 6 HOH B 52 452 452 HOH HOH . 
K 6 HOH B 53 453 453 HOH HOH . 
K 6 HOH B 54 454 454 HOH HOH . 
K 6 HOH B 55 455 455 HOH HOH . 
K 6 HOH B 56 456 456 HOH HOH . 
K 6 HOH B 57 457 457 HOH HOH . 
K 6 HOH B 58 458 458 HOH HOH . 
K 6 HOH B 59 459 459 HOH HOH . 
K 6 HOH B 60 460 460 HOH HOH . 
K 6 HOH B 61 461 461 HOH HOH . 
K 6 HOH B 62 462 462 HOH HOH . 
K 6 HOH B 63 463 463 HOH HOH . 
K 6 HOH B 64 464 464 HOH HOH . 
K 6 HOH B 65 465 465 HOH HOH . 
K 6 HOH B 66 466 466 HOH HOH . 
K 6 HOH B 67 467 467 HOH HOH . 
K 6 HOH B 68 468 468 HOH HOH . 
K 6 HOH B 69 469 469 HOH HOH . 
K 6 HOH B 70 470 470 HOH HOH . 
K 6 HOH B 71 471 471 HOH HOH . 
K 6 HOH B 72 472 472 HOH HOH . 
K 6 HOH B 73 473 473 HOH HOH . 
K 6 HOH B 74 474 474 HOH HOH . 
K 6 HOH B 75 475 475 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 3 5.427 -4.8 8.193 1 46.66 ? PB ADP 302 A 1 
HETATM 2 O O1B ADP . . . D 3 4.172 -5.317 7.509 1 40.02 ? O1B ADP 302 A 1 
HETATM 3 O O2B ADP . . . D 3 5.28 -4.439 9.672 1 45.13 ? O2B ADP 302 A 1 
HETATM 4 O O3B ADP . . . D 3 6.258 -3.818 7.369 1 44.7 ? O3B ADP 302 A 1 
HETATM 5 P PA ADP . . . D 3 6.925 -6.906 7.043 1 40.56 ? PA ADP 302 A 1 
HETATM 6 O O1A ADP . . . D 3 5.845 -6.992 5.997 1 37.89 ? O1A ADP 302 A 1 
HETATM 7 O O2A ADP . . . D 3 8.281 -6.303 6.716 1 34.52 ? O2A ADP 302 A 1 
HETATM 8 O O3A ADP . . . D 3 6.35 -6.11 8.315 1 44.58 ? O3A ADP 302 A 1 
HETATM 9 O O5' ADP . . . D 3 7.033 -8.326 7.79 1 38.14 ? O5' ADP 302 A 1 
HETATM 10 C C5' ADP . . . D 3 8.252 -8.622 8.442 1 38.58 ? C5' ADP 302 A 1 
HETATM 11 C C4' ADP . . . D 3 8.02 -8.78 9.921 1 40.08 ? C4' ADP 302 A 1 
HETATM 12 O O4' ADP . . . D 3 9.13 -9.539 10.39 1 41.51 ? O4' ADP 302 A 1 
HETATM 13 C C3' ADP . . . D 3 8.065 -7.444 10.656 1 40.36 ? C3' ADP 302 A 1 
HETATM 14 O O3' ADP . . . D 3 7.196 -7.513 11.801 1 35.37 ? O3' ADP 302 A 1 
HETATM 15 C C2' ADP . . . D 3 9.525 -7.336 11.077 1 41.27 ? C2' ADP 302 A 1 
HETATM 16 O O2' ADP . . . D 3 9.78 -6.534 12.24 1 41.71 ? O2' ADP 302 A 1 
HETATM 17 C C1' ADP . . . D 3 9.878 -8.783 11.342 1 39.79 ? C1' ADP 302 A 1 
HETATM 18 N N9 ADP . . . D 3 11.317 -9.054 11.171 1 37.79 ? N9 ADP 302 A 1 
HETATM 19 C C8 ADP . . . D 3 12.187 -8.412 10.374 1 35.15 ? C8 ADP 302 A 1 
HETATM 20 N N7 ADP . . . D 3 13.427 -8.959 10.484 1 34.56 ? N7 ADP 302 A 1 
HETATM 21 C C5 ADP . . . D 3 13.352 -9.99 11.359 1 35.71 ? C5 ADP 302 A 1 
HETATM 22 C C6 ADP . . . D 3 14.283 -11.003 11.915 1 33.69 ? C6 ADP 302 A 1 
HETATM 23 N N6 ADP . . . D 3 15.586 -11.022 11.548 1 35.62 ? N6 ADP 302 A 1 
HETATM 24 N N1 ADP . . . D 3 13.801 -11.898 12.795 1 32.95 ? N1 ADP 302 A 1 
HETATM 25 C C2 ADP . . . D 3 12.496 -11.905 13.145 1 36.68 ? C2 ADP 302 A 1 
HETATM 26 N N3 ADP . . . D 3 11.571 -11.025 12.686 1 36.73 ? N3 ADP 302 A 1 
HETATM 27 C C4 ADP . . . D 3 11.947 -10.051 11.807 1 37.83 ? C4 ADP 302 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#