data_4P31 # _model_server_result.job_id SI5RfvY5TYhpMQqvInx8LQ _model_server_result.datetime_utc '2024-11-16 19:31:42' _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 4p31 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4P31 # _exptl.entry_id 4P31 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.83 _cell.angle_gamma 90 _cell.entry_id 4P31 _cell.length_a 192.6 _cell.length_b 35.88 _cell.length_c 64.34 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P31 _symmetry.cell_setting . _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,G 1 1 B,E,F,H 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 C N N ? 2 E 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 covale ? covale1 A C TYR 46 A TYR 47 1_555 A N MSE 47 A MSE 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C MSE 47 A MSE 48 1_555 A N VAL 48 A VAL 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C LEU 98 A LEU 99 1_555 A N MSE 99 A MSE 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 99 A MSE 100 1_555 A N ALA 100 A ALA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C LEU 120 A LEU 121 1_555 A N MSE 121 A MSE 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 121 A MSE 122 1_555 A N GLU 122 A GLU 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C SER 132 A SER 133 1_555 A N MSE 133 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 133 A MSE 134 1_555 A N GLY 134 A GLY 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 B C TYR 46 B TYR 47 1_555 B N MSE 47 B MSE 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale10 B C MSE 47 B MSE 48 1_555 B N VAL 48 B VAL 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 B C LEU 98 B LEU 99 1_555 B N MSE 99 B MSE 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 B C MSE 99 B MSE 100 1_555 B N ALA 100 B ALA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 B C LEU 120 B LEU 121 1_555 B N MSE 121 B MSE 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 B C MSE 121 B MSE 122 1_555 B N GLU 122 B GLU 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale15 B C SER 132 B SER 133 1_555 B N MSE 133 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C MSE 133 B MSE 134 1_555 B N GLY 134 B GLY 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OG1 THR 42 A THR 43 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 A OE1 GLN 84 A GLN 85 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc3 C O3B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc4 D MG MG . A MG 402 1_555 G O HOH . A HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 D MG MG . A MG 402 1_555 G O HOH . A HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc6 D MG MG . A MG 402 1_555 G O HOH . A HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B OG1 THR 42 B THR 43 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc8 B OE1 GLN 84 B GLN 85 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 E O1B ADP . B ADP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc10 F MG MG . B MG 402 1_555 H O HOH . B HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc11 F MG MG . B MG 402 1_555 H O HOH . B HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc12 F MG MG . B MG 402 1_555 H O HOH . B HOH 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _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 4P31 _atom_sites.fract_transf_matrix[1][1] 0.005192 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00053 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027871 _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] 0.015623 _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 ADP A 1 401 401 ADP ADP . D 3 MG A 1 402 1 MG MG . E 2 ADP B 1 401 401 ADP ADP . F 3 MG B 1 402 2 MG MG . G 4 HOH A 1 501 23 HOH HOH . G 4 HOH A 2 502 71 HOH HOH . G 4 HOH A 3 503 44 HOH HOH . G 4 HOH A 4 504 31 HOH HOH . G 4 HOH A 5 505 8 HOH HOH . G 4 HOH A 6 506 34 HOH HOH . G 4 HOH A 7 507 37 HOH HOH . G 4 HOH A 8 508 9 HOH HOH . G 4 HOH A 9 509 95 HOH HOH . G 4 HOH A 10 510 59 HOH HOH . G 4 HOH A 11 511 55 HOH HOH . G 4 HOH A 12 512 94 HOH HOH . G 4 HOH A 13 513 45 HOH HOH . G 4 HOH A 14 514 79 HOH HOH . G 4 HOH A 15 515 51 HOH HOH . G 4 HOH A 16 516 84 HOH HOH . G 4 HOH A 17 517 98 HOH HOH . G 4 HOH A 18 518 3 HOH HOH . G 4 HOH A 19 519 5 HOH HOH . G 4 HOH A 20 520 7 HOH HOH . G 4 HOH A 21 521 10 HOH HOH . G 4 HOH A 22 522 11 HOH HOH . G 4 HOH A 23 523 12 HOH HOH . G 4 HOH A 24 524 13 HOH HOH . G 4 HOH A 25 525 14 HOH HOH . G 4 HOH A 26 526 15 HOH HOH . G 4 HOH A 27 527 16 HOH HOH . G 4 HOH A 28 528 17 HOH HOH . G 4 HOH A 29 529 20 HOH HOH . G 4 HOH A 30 530 24 HOH HOH . G 4 HOH A 31 531 30 HOH HOH . G 4 HOH A 32 532 32 HOH HOH . G 4 HOH A 33 533 35 HOH HOH . G 4 HOH A 34 534 36 HOH HOH . G 4 HOH A 35 535 38 HOH HOH . G 4 HOH A 36 536 40 HOH HOH . G 4 HOH A 37 537 42 HOH HOH . G 4 HOH A 38 538 46 HOH HOH . G 4 HOH A 39 539 48 HOH HOH . G 4 HOH A 40 540 49 HOH HOH . G 4 HOH A 41 541 52 HOH HOH . G 4 HOH A 42 542 60 HOH HOH . G 4 HOH A 43 543 64 HOH HOH . G 4 HOH A 44 544 65 HOH HOH . G 4 HOH A 45 545 73 HOH HOH . G 4 HOH A 46 546 75 HOH HOH . G 4 HOH A 47 547 76 HOH HOH . G 4 HOH A 48 548 78 HOH HOH . G 4 HOH A 49 549 80 HOH HOH . G 4 HOH A 50 550 83 HOH HOH . G 4 HOH A 51 551 87 HOH HOH . G 4 HOH A 52 552 91 HOH HOH . G 4 HOH A 53 553 92 HOH HOH . G 4 HOH A 54 554 96 HOH HOH . G 4 HOH A 55 555 102 HOH HOH . G 4 HOH A 56 556 103 HOH HOH . G 4 HOH A 57 557 104 HOH HOH . H 4 HOH B 1 501 22 HOH HOH . H 4 HOH B 2 502 50 HOH HOH . H 4 HOH B 3 503 43 HOH HOH . H 4 HOH B 4 504 90 HOH HOH . H 4 HOH B 5 505 58 HOH HOH . H 4 HOH B 6 506 61 HOH HOH . H 4 HOH B 7 507 27 HOH HOH . H 4 HOH B 8 508 82 HOH HOH . H 4 HOH B 9 509 97 HOH HOH . H 4 HOH B 10 510 54 HOH HOH . H 4 HOH B 11 511 106 HOH HOH . H 4 HOH B 12 512 53 HOH HOH . H 4 HOH B 13 513 89 HOH HOH . H 4 HOH B 14 514 88 HOH HOH . H 4 HOH B 15 515 86 HOH HOH . H 4 HOH B 16 516 1 HOH HOH . H 4 HOH B 17 517 2 HOH HOH . H 4 HOH B 18 518 4 HOH HOH . H 4 HOH B 19 519 6 HOH HOH . H 4 HOH B 20 520 18 HOH HOH . H 4 HOH B 21 521 19 HOH HOH . H 4 HOH B 22 522 21 HOH HOH . H 4 HOH B 23 523 25 HOH HOH . H 4 HOH B 24 524 26 HOH HOH . H 4 HOH B 25 525 28 HOH HOH . H 4 HOH B 26 526 29 HOH HOH . H 4 HOH B 27 527 33 HOH HOH . H 4 HOH B 28 528 39 HOH HOH . H 4 HOH B 29 529 41 HOH HOH . H 4 HOH B 30 530 47 HOH HOH . H 4 HOH B 31 531 56 HOH HOH . H 4 HOH B 32 532 57 HOH HOH . H 4 HOH B 33 533 62 HOH HOH . H 4 HOH B 34 534 63 HOH HOH . H 4 HOH B 35 535 66 HOH HOH . H 4 HOH B 36 536 67 HOH HOH . H 4 HOH B 37 537 68 HOH HOH . H 4 HOH B 38 538 69 HOH HOH . H 4 HOH B 39 539 70 HOH HOH . H 4 HOH B 40 540 72 HOH HOH . H 4 HOH B 41 541 74 HOH HOH . H 4 HOH B 42 542 77 HOH HOH . H 4 HOH B 43 543 81 HOH HOH . H 4 HOH B 44 544 85 HOH HOH . H 4 HOH B 45 545 93 HOH HOH . H 4 HOH B 46 546 99 HOH HOH . H 4 HOH B 47 547 100 HOH HOH . H 4 HOH B 48 548 101 HOH HOH . H 4 HOH B 49 549 105 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 2 56.128 37.928 15.602 1 24.07 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 2 55.667 37.538 14.211 1 24.97 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 2 56.735 39.307 15.669 1 23.95 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 2 56.891 36.835 16.319 1 21.57 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 2 54.553 37.403 17.949 1 25.98 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 2 54.022 36.003 17.768 1 24.14 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 2 55.774 37.63 18.81 1 24.82 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 2 54.765 38.045 16.468 1 24.65 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 2 53.398 38.336 18.582 1 27.62 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 2 52.149 38.565 17.926 1 27.42 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 2 51.372 39.619 18.709 1 27.57 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 2 50.969 39.083 19.972 1 25.33 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 2 52.237 40.835 19.009 1 36.14 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 2 51.487 42.008 18.691 1 38.65 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 2 52.497 40.779 20.504 1 28.89 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 2 52.566 42.075 21.095 1 30.09 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 2 51.312 39.992 21.026 1 25.04 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 2 51.659 39.245 22.261 1 38.36 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 2 52.66 38.349 22.398 1 36.85 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 2 52.696 37.85 23.661 1 36.6 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 2 51.701 38.436 24.355 1 38.3 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 2 51.177 38.365 25.739 1 43.25 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 2 51.742 37.547 26.66 1 42.2 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 2 50.118 39.145 26.049 1 43.48 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 2 49.547 39.964 25.146 1 44.69 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 2 49.967 40.077 23.875 1 41.19 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 2 51.023 39.355 23.429 1 38.11 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #