data_5NBL # _model_server_result.job_id dLDkv0ww8H_SmrX2jAdcRQ _model_server_result.datetime_utc '2024-12-27 03:28:42' _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 5nbl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":502}' # _entry.id 5NBL # _exptl.entry_id 5NBL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 5NBL _cell.length_a 191.224 _cell.length_b 191.224 _cell.length_c 221.973 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NBL _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_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,F,H,I,J,M,P,R 1 1 B,C,E,G,K,L,N,O,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 ? 6 J N N ? 6 L 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 disulf ? disulf1 E SG CYS 24 E CYS 24 1_555 E SG CYS 98 E CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 F SG CYS 24 F CYS 24 1_555 F SG CYS 98 F CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 I CA CA . A CA 501 1_555 J O1G ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc2 I CA CA . A CA 501 1_555 J O2B ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 I CA CA . A CA 501 1_555 M O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc4 I CA CA . A CA 501 1_555 M O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc5 K CA CA . B CA 501 1_555 L O2G ATP . B ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc6 K CA CA . B CA 501 1_555 L O1B ATP . B ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc7 K CA CA . B CA 501 1_555 N O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc8 K CA CA . B CA 501 1_555 N O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5NBL _atom_sites.fract_transf_matrix[1][1] 0.005229 _atom_sites.fract_transf_matrix[1][2] 0.003019 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006038 _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] 0.004505 _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 I 5 CA A 1 501 501 CA CA . J 6 ATP A 1 502 502 ATP ATP . K 5 CA B 1 501 501 CA CA . L 6 ATP B 1 502 502 ATP ATP . M 7 HOH A 1 601 14 HOH HOH . M 7 HOH A 2 602 69 HOH HOH . M 7 HOH A 3 603 23 HOH HOH . M 7 HOH A 4 604 20 HOH HOH . M 7 HOH A 5 605 96 HOH HOH . M 7 HOH A 6 606 108 HOH HOH . M 7 HOH A 7 607 13 HOH HOH . M 7 HOH A 8 608 49 HOH HOH . M 7 HOH A 9 609 105 HOH HOH . M 7 HOH A 10 610 118 HOH HOH . M 7 HOH A 11 611 77 HOH HOH . M 7 HOH A 12 612 113 HOH HOH . M 7 HOH A 13 613 19 HOH HOH . M 7 HOH A 14 614 62 HOH HOH . M 7 HOH A 15 615 51 HOH HOH . M 7 HOH A 16 616 73 HOH HOH . M 7 HOH A 17 617 90 HOH HOH . M 7 HOH A 18 618 101 HOH HOH . M 7 HOH A 19 619 40 HOH HOH . M 7 HOH A 20 620 31 HOH HOH . M 7 HOH A 21 621 43 HOH HOH . M 7 HOH A 22 622 16 HOH HOH . M 7 HOH A 23 623 34 HOH HOH . M 7 HOH A 24 624 119 HOH HOH . M 7 HOH A 25 625 26 HOH HOH . M 7 HOH A 26 626 6 HOH HOH . M 7 HOH A 27 627 112 HOH HOH . M 7 HOH A 28 628 86 HOH HOH . M 7 HOH A 29 629 110 HOH HOH . M 7 HOH A 30 630 9 HOH HOH . M 7 HOH A 31 631 71 HOH HOH . M 7 HOH A 32 632 3 HOH HOH . N 7 HOH B 1 601 17 HOH HOH . N 7 HOH B 2 602 68 HOH HOH . N 7 HOH B 3 603 56 HOH HOH . N 7 HOH B 4 604 74 HOH HOH . N 7 HOH B 5 605 47 HOH HOH . N 7 HOH B 6 606 29 HOH HOH . N 7 HOH B 7 607 48 HOH HOH . N 7 HOH B 8 608 100 HOH HOH . N 7 HOH B 9 609 54 HOH HOH . N 7 HOH B 10 610 22 HOH HOH . N 7 HOH B 11 611 97 HOH HOH . N 7 HOH B 12 612 55 HOH HOH . N 7 HOH B 13 613 53 HOH HOH . N 7 HOH B 14 614 39 HOH HOH . N 7 HOH B 15 615 33 HOH HOH . N 7 HOH B 16 616 117 HOH HOH . N 7 HOH B 17 617 65 HOH HOH . N 7 HOH B 18 618 64 HOH HOH . N 7 HOH B 19 619 103 HOH HOH . N 7 HOH B 20 620 4 HOH HOH . N 7 HOH B 21 621 28 HOH HOH . N 7 HOH B 22 622 91 HOH HOH . N 7 HOH B 23 623 2 HOH HOH . N 7 HOH B 24 624 114 HOH HOH . N 7 HOH B 25 625 24 HOH HOH . N 7 HOH B 26 626 38 HOH HOH . N 7 HOH B 27 627 85 HOH HOH . N 7 HOH B 28 628 109 HOH HOH . N 7 HOH B 29 629 5 HOH HOH . N 7 HOH B 30 630 61 HOH HOH . N 7 HOH B 31 631 75 HOH HOH . N 7 HOH B 32 632 8 HOH HOH . O 7 HOH C 1 401 116 HOH HOH . O 7 HOH C 2 402 89 HOH HOH . O 7 HOH C 3 403 50 HOH HOH . O 7 HOH C 4 404 11 HOH HOH . O 7 HOH C 5 405 10 HOH HOH . O 7 HOH C 6 406 60 HOH HOH . O 7 HOH C 7 407 80 HOH HOH . O 7 HOH C 8 408 35 HOH HOH . O 7 HOH C 9 409 115 HOH HOH . O 7 HOH C 10 410 76 HOH HOH . O 7 HOH C 11 411 42 HOH HOH . O 7 HOH C 12 412 82 HOH HOH . O 7 HOH C 13 413 21 HOH HOH . O 7 HOH C 14 414 15 HOH HOH . O 7 HOH C 15 415 78 HOH HOH . O 7 HOH C 16 416 25 HOH HOH . O 7 HOH C 17 417 70 HOH HOH . O 7 HOH C 18 418 58 HOH HOH . O 7 HOH C 19 419 7 HOH HOH . P 7 HOH D 1 401 30 HOH HOH . P 7 HOH D 2 402 92 HOH HOH . P 7 HOH D 3 403 88 HOH HOH . P 7 HOH D 4 404 84 HOH HOH . P 7 HOH D 5 405 59 HOH HOH . P 7 HOH D 6 406 66 HOH HOH . P 7 HOH D 7 407 44 HOH HOH . P 7 HOH D 8 408 37 HOH HOH . P 7 HOH D 9 409 99 HOH HOH . P 7 HOH D 10 410 36 HOH HOH . P 7 HOH D 11 411 79 HOH HOH . P 7 HOH D 12 412 98 HOH HOH . P 7 HOH D 13 413 106 HOH HOH . P 7 HOH D 14 414 52 HOH HOH . P 7 HOH D 15 415 102 HOH HOH . P 7 HOH D 16 416 93 HOH HOH . P 7 HOH D 17 417 83 HOH HOH . P 7 HOH D 18 418 94 HOH HOH . P 7 HOH D 19 419 1 HOH HOH . P 7 HOH D 20 420 87 HOH HOH . P 7 HOH D 21 421 67 HOH HOH . P 7 HOH D 22 422 32 HOH HOH . P 7 HOH D 23 423 18 HOH HOH . P 7 HOH D 24 424 41 HOH HOH . Q 7 HOH E 1 201 81 HOH HOH . Q 7 HOH E 2 202 111 HOH HOH . Q 7 HOH E 3 203 27 HOH HOH . Q 7 HOH E 4 204 107 HOH HOH . Q 7 HOH E 5 205 63 HOH HOH . Q 7 HOH E 6 206 45 HOH HOH . Q 7 HOH E 7 207 46 HOH HOH . R 7 HOH F 1 201 72 HOH HOH . R 7 HOH F 2 202 95 HOH HOH . R 7 HOH F 3 203 57 HOH HOH . R 7 HOH F 4 204 104 HOH HOH . R 7 HOH F 5 205 12 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 PG ATP . . . L 6 -29.31 200.591 -4.686 1 37.88 ? PG ATP 502 B 1 HETATM 2 O O1G ATP . . . L 6 -28.114 201.011 -5.503 1 46.77 ? O1G ATP 502 B 1 HETATM 3 O O2G ATP . . . L 6 -29.864 201.702 -3.824 1 50.57 ? O2G ATP 502 B 1 HETATM 4 O O3G ATP . . . L 6 -30.336 199.807 -5.462 1 39.15 ? O3G ATP 502 B 1 HETATM 5 P PB ATP . . . L 6 -28.894 199.489 -2.085 1 35.67 ? PB ATP 502 B 1 HETATM 6 O O1B ATP . . . L 6 -30.084 200.342 -1.721 1 44.03 ? O1B ATP 502 B 1 HETATM 7 O O2B ATP . . . L 6 -28.838 198.049 -1.657 1 37.18 ? O2B ATP 502 B 1 HETATM 8 O O3B ATP . . . L 6 -28.651 199.51 -3.68 1 48.08 ? O3B ATP 502 B 1 HETATM 9 P PA ATP . . . L 6 -27.406 200.964 -0.171 1 35.8 ? PA ATP 502 B 1 HETATM 10 O O1A ATP . . . L 6 -28.104 202.293 -0.291 1 42.05 ? O1A ATP 502 B 1 HETATM 11 O O2A ATP . . . L 6 -27.73 200.017 0.954 1 37.02 ? O2A ATP 502 B 1 HETATM 12 O O3A ATP . . . L 6 -27.541 200.186 -1.569 1 36.67 ? O3A ATP 502 B 1 HETATM 13 O O5' ATP . . . L 6 -25.838 201.302 -0.111 1 31.35 ? O5' ATP 502 B 1 HETATM 14 C C5' ATP . . . L 6 -24.849 200.34 -0.471 1 36.39 ? C5' ATP 502 B 1 HETATM 15 C C4' ATP . . . L 6 -23.578 201.08 -0.852 1 37.78 ? C4' ATP 502 B 1 HETATM 16 O O4' ATP . . . L 6 -23.172 201.924 0.23 1 36.68 ? O4' ATP 502 B 1 HETATM 17 C C3' ATP . . . L 6 -22.416 200.14 -1.137 1 40.88 ? C3' ATP 502 B 1 HETATM 18 O O3' ATP . . . L 6 -21.743 200.528 -2.345 1 30.29 ? O3' ATP 502 B 1 HETATM 19 C C2' ATP . . . L 6 -21.502 200.315 0.056 1 38.14 ? C2' ATP 502 B 1 HETATM 20 O O2' ATP . . . L 6 -20.124 200.088 -0.245 1 41.32 ? O2' ATP 502 B 1 HETATM 21 C C1' ATP . . . L 6 -21.772 201.752 0.45 1 33.43 ? C1' ATP 502 B 1 HETATM 22 N N9 ATP . . . L 6 -21.403 202.03 1.856 1 39.3 ? N9 ATP 502 B 1 HETATM 23 C C8 ATP . . . L 6 -21.792 201.339 2.945 1 31.44 ? C8 ATP 502 B 1 HETATM 24 N N7 ATP . . . L 6 -21.261 201.885 4.07 1 35.58 ? N7 ATP 502 B 1 HETATM 25 C C5 ATP . . . L 6 -20.522 202.947 3.696 1 37.38 ? C5 ATP 502 B 1 HETATM 26 C C6 ATP . . . L 6 -19.695 203.963 4.376 1 31.39 ? C6 ATP 502 B 1 HETATM 27 N N6 ATP . . . L 6 -19.558 203.942 5.722 1 39 ? N6 ATP 502 B 1 HETATM 28 N N1 ATP . . . L 6 -19.089 204.899 3.61 1 38.5 ? N1 ATP 502 B 1 HETATM 29 C C2 ATP . . . L 6 -19.222 204.928 2.269 1 35.93 ? C2 ATP 502 B 1 HETATM 30 N N3 ATP . . . L 6 -19.959 204.033 1.59 1 30.83 ? N3 ATP 502 B 1 HETATM 31 C C4 ATP . . . L 6 -20.619 203.039 2.236 1 36.24 ? C4 ATP 502 B 1 HETATM 32 H "H5'1" ATP . . . L 6 -25.2 199.741 -1.313 1 43.66 ? "H5'1" ATP 502 B 1 HETATM 33 H "H5'2" ATP . . . L 6 -24.655 199.672 0.371 1 43.66 ? "H5'2" ATP 502 B 1 HETATM 34 H H4' ATP . . . L 6 -23.773 201.686 -1.748 1 45.34 ? H4' ATP 502 B 1 HETATM 35 H H3' ATP . . . L 6 -22.773 199.102 -1.191 1 49.05 ? H3' ATP 502 B 1 HETATM 36 H HO3' ATP . . . L 6 -21.007 199.922 -2.513 1 36.35 ? HO3' ATP 502 B 1 HETATM 37 H H2' ATP . . . L 6 -21.832 199.65 0.866 1 45.77 ? H2' ATP 502 B 1 HETATM 38 H HO2' ATP . . . L 6 -20.006 199.176 -0.546 1 49.58 ? HO2' ATP 502 B 1 HETATM 39 H H1' ATP . . . L 6 -21.206 202.413 -0.221 1 40.12 ? H1' ATP 502 B 1 HETATM 40 H H8 ATP . . . L 6 -22.437 200.468 2.927 1 37.72 ? H8 ATP 502 B 1 HETATM 41 H HN61 ATP . . . L 6 -18.991 204.639 6.183 1 46.8 ? HN61 ATP 502 B 1 HETATM 42 H HN62 ATP . . . L 6 -20.022 203.228 6.266 1 46.8 ? HN62 ATP 502 B 1 HETATM 43 H H2 ATP . . . L 6 -18.711 205.705 1.714 1 43.11 ? H2 ATP 502 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #