data_5GRE
#
_model_server_result.job_id            RWeCDskIF7a4Rxg0AJdohQ 
_model_server_result.datetime_utc      '2025-07-16 08:56:53' 
_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          5gre 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    5GRE 
#
_exptl.entry_id    5GRE 
_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            "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         120 
_cell.entry_id            5GRE 
_cell.length_a            104.91 
_cell.length_b            104.91 
_cell.length_c            146.25 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GRE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 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 
_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                      4 
_struct_asym.id                             D 
_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 OD1 ASP 230 A ASP 230 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? 
metalc ? metalc2 A OD2 ASP 234 A ASP 234 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc3 C MG MG . A MG 401 1_555 G O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? 
metalc ? metalc4 C MG MG . A MG 401 1_555 B OD2 ASP 215 B ASP 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc5 B OD1 ASN 78 B ASN 78 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc6 B O ARG 272 B ARG 272 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc7 D O3B ADP . B ADP 401 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc8 E MG MG . B MG 402 1_555 F O5 CIT . B CIT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc9 E MG MG . B MG 402 1_555 H O HOH . B HOH 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
#
_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                     5GRE 
_atom_sites.fract_transf_matrix[1][1]    0.009532 
_atom_sites.fract_transf_matrix[1][2]    0.005503 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011007 
_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]    0.006838 
_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 3 MG A 1 401 1 MG MG . 
D 4 ADP B 1 401 1 ADP ADP . 
E 3 MG B 1 402 1 MG MG . 
F 5 CIT B 1 403 1 CIT CIT . 
G 6 HOH A 1 501 97 HOH HOH . 
G 6 HOH A 2 502 28 HOH HOH . 
G 6 HOH A 3 503 24 HOH HOH . 
G 6 HOH A 4 504 72 HOH HOH . 
G 6 HOH A 5 505 99 HOH HOH . 
G 6 HOH A 6 506 58 HOH HOH . 
G 6 HOH A 7 507 70 HOH HOH . 
G 6 HOH A 8 508 94 HOH HOH . 
G 6 HOH A 9 509 29 HOH HOH . 
G 6 HOH A 10 510 30 HOH HOH . 
G 6 HOH A 11 511 82 HOH HOH . 
H 6 HOH B 1 501 108 HOH HOH . 
H 6 HOH B 2 502 6 HOH HOH . 
H 6 HOH B 3 503 39 HOH HOH . 
H 6 HOH B 4 504 25 HOH HOH . 
H 6 HOH B 5 505 43 HOH HOH . 
H 6 HOH B 6 506 4 HOH HOH . 
H 6 HOH B 7 507 11 HOH HOH . 
H 6 HOH B 8 508 3 HOH HOH . 
H 6 HOH B 9 509 66 HOH HOH . 
H 6 HOH B 10 510 69 HOH HOH . 
H 6 HOH B 11 511 53 HOH HOH . 
H 6 HOH B 12 512 16 HOH HOH . 
H 6 HOH B 13 513 41 HOH HOH . 
H 6 HOH B 14 514 5 HOH HOH . 
H 6 HOH B 15 515 56 HOH HOH . 
H 6 HOH B 16 516 13 HOH HOH . 
H 6 HOH B 17 517 47 HOH HOH . 
H 6 HOH B 18 518 1 HOH HOH . 
H 6 HOH B 19 519 102 HOH HOH . 
H 6 HOH B 20 520 33 HOH HOH . 
H 6 HOH B 21 521 7 HOH HOH . 
H 6 HOH B 22 522 22 HOH HOH . 
H 6 HOH B 23 523 65 HOH HOH . 
H 6 HOH B 24 524 32 HOH HOH . 
H 6 HOH B 25 525 21 HOH HOH . 
H 6 HOH B 26 526 106 HOH HOH . 
H 6 HOH B 27 527 46 HOH HOH . 
H 6 HOH B 28 528 55 HOH HOH . 
H 6 HOH B 29 529 17 HOH HOH . 
H 6 HOH B 30 530 19 HOH HOH . 
H 6 HOH B 31 531 18 HOH HOH . 
H 6 HOH B 32 532 107 HOH HOH . 
H 6 HOH B 33 533 10 HOH HOH . 
H 6 HOH B 34 534 9 HOH HOH . 
H 6 HOH B 35 535 23 HOH HOH . 
H 6 HOH B 36 536 2 HOH HOH . 
H 6 HOH B 37 537 103 HOH HOH . 
H 6 HOH B 38 538 93 HOH HOH . 
H 6 HOH B 39 539 14 HOH HOH . 
H 6 HOH B 40 540 26 HOH HOH . 
H 6 HOH B 41 541 64 HOH HOH . 
H 6 HOH B 42 542 20 HOH HOH . 
H 6 HOH B 43 543 42 HOH HOH . 
H 6 HOH B 44 544 15 HOH HOH . 
H 6 HOH B 45 545 73 HOH HOH . 
H 6 HOH B 46 546 68 HOH HOH . 
H 6 HOH B 47 547 35 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 4 4.648 41.904 -24.431 1 54.46 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . D 4 4.884 40.89 -25.563 1 49.87 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . D 4 4.112 41.215 -23.211 1 52.25 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . D 4 5.965 42.626 -24.122 1 49.13 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . D 4 2.177 42.826 -25.644 1 35.95 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . D 4 2.532 42.741 -27.105 1 32.48 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . D 4 1.44 41.626 -25.161 1 29.61 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . D 4 3.548 43.012 -24.821 1 52 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . D 4 1.327 44.126 -25.411 1 38.18 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . D 4 0.141 44.111 -24.638 1 33.42 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . D 4 -1.053 44.646 -25.412 1 36.07 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . D 4 -0.939 46.106 -25.729 1 33.75 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . D 4 -1.23 43.965 -26.686 1 39.63 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . D 4 -2.688 43.773 -26.885 1 37.49 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . D 4 -0.682 44.84 -27.697 1 41.05 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . D 4 -1.292 44.542 -29.032 1 42.67 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . D 4 -1.079 46.151 -27.209 1 35.71 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . D 4 -0.254 47.14 -27.67 1 38.4 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . D 4 1.01 47.397 -27.287 1 37.46 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . D 4 1.487 48.443 -27.949 1 35.38 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . D 4 0.53 48.895 -28.763 1 33.13 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . D 4 0.455 49.942 -29.68 1 36.02 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . D 4 1.552 50.792 -29.876 1 32.63 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . D 4 -0.681 50.146 -30.372 1 32.8 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . D 4 -1.752 49.346 -30.211 1 33.98 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . D 4 -1.72 48.303 -29.321 1 31.58 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . D 4 -0.608 48.076 -28.607 1 34.36 ? C4 ADP 401 B 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#