data_3SP1 # _model_server_result.job_id JQJw8U-otIr2BgmFchPVfg _model_server_result.datetime_utc '2024-12-25 16:29:11' _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 3sp1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":482}' # _entry.id 3SP1 # _exptl.entry_id 3SP1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 93.18 _cell.angle_gamma 90 _cell.entry_id 3SP1 _cell.length_a 62.62 _cell.length_b 49.89 _cell.length_c 179.63 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SP1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,H 1 1 B,E,F,G,I 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 ? 3 D N N ? 3 F 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 A SG CYS 48 A CYS 27 1_555 C ZN ZN . A ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc2 A SG CYS 242 A CYS 221 1_555 C ZN ZN . A ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 A NE2 HIS 267 A HIS 246 1_555 C ZN ZN . A ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 C ZN ZN . A ZN 481 1_555 H O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc5 B SG CYS 48 B CYS 27 1_555 E ZN ZN . B ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc6 B SG CYS 242 B CYS 221 1_555 E ZN ZN . B ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc7 B NE2 HIS 267 B HIS 246 1_555 E ZN ZN . B ZN 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 E ZN ZN . B ZN 481 1_555 I O HOH . B HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3SP1 _atom_sites.fract_transf_matrix[1][1] 0.015969 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000887 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020044 _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] 0.005576 _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 ZN A 1 481 481 ZN ZN . D 3 AMP A 1 482 482 AMP AMP . E 2 ZN B 1 481 481 ZN ZN . F 3 AMP B 1 482 482 AMP AMP . G 4 CL B 1 483 483 CL CL . H 5 HOH A 1 483 483 HOH HOH . H 5 HOH A 2 484 484 HOH HOH . H 5 HOH A 3 485 485 HOH HOH . H 5 HOH A 4 486 486 HOH HOH . H 5 HOH A 5 487 487 HOH HOH . H 5 HOH A 6 488 488 HOH HOH . H 5 HOH A 7 489 489 HOH HOH . H 5 HOH A 8 490 490 HOH HOH . H 5 HOH A 9 491 491 HOH HOH . H 5 HOH A 10 492 492 HOH HOH . H 5 HOH A 11 493 493 HOH HOH . H 5 HOH A 12 494 494 HOH HOH . H 5 HOH A 13 495 495 HOH HOH . H 5 HOH A 14 496 496 HOH HOH . H 5 HOH A 15 497 497 HOH HOH . H 5 HOH A 16 498 498 HOH HOH . H 5 HOH A 17 499 499 HOH HOH . H 5 HOH A 18 500 500 HOH HOH . H 5 HOH A 19 501 501 HOH HOH . H 5 HOH A 20 502 502 HOH HOH . H 5 HOH A 21 503 503 HOH HOH . H 5 HOH A 22 504 504 HOH HOH . H 5 HOH A 23 505 505 HOH HOH . H 5 HOH A 24 506 506 HOH HOH . H 5 HOH A 25 507 507 HOH HOH . H 5 HOH A 26 508 508 HOH HOH . H 5 HOH A 27 509 509 HOH HOH . H 5 HOH A 28 510 510 HOH HOH . H 5 HOH A 29 511 511 HOH HOH . H 5 HOH A 30 512 512 HOH HOH . H 5 HOH A 31 513 513 HOH HOH . H 5 HOH A 32 514 514 HOH HOH . H 5 HOH A 33 515 515 HOH HOH . H 5 HOH A 34 516 516 HOH HOH . H 5 HOH A 35 517 517 HOH HOH . H 5 HOH A 36 518 518 HOH HOH . H 5 HOH A 37 519 519 HOH HOH . H 5 HOH A 38 520 520 HOH HOH . H 5 HOH A 39 521 521 HOH HOH . H 5 HOH A 40 522 522 HOH HOH . H 5 HOH A 41 523 523 HOH HOH . H 5 HOH A 42 524 524 HOH HOH . H 5 HOH A 43 525 525 HOH HOH . H 5 HOH A 44 526 526 HOH HOH . H 5 HOH A 45 527 527 HOH HOH . H 5 HOH A 46 528 528 HOH HOH . H 5 HOH A 47 529 529 HOH HOH . H 5 HOH A 48 530 530 HOH HOH . H 5 HOH A 49 531 531 HOH HOH . H 5 HOH A 50 532 532 HOH HOH . H 5 HOH A 51 533 533 HOH HOH . H 5 HOH A 52 534 534 HOH HOH . H 5 HOH A 53 535 535 HOH HOH . H 5 HOH A 54 536 536 HOH HOH . H 5 HOH A 55 537 537 HOH HOH . H 5 HOH A 56 538 538 HOH HOH . H 5 HOH A 57 539 539 HOH HOH . H 5 HOH A 58 540 540 HOH HOH . H 5 HOH A 59 541 541 HOH HOH . H 5 HOH A 60 542 542 HOH HOH . H 5 HOH A 61 543 543 HOH HOH . H 5 HOH A 62 544 544 HOH HOH . H 5 HOH A 63 545 545 HOH HOH . H 5 HOH A 64 546 546 HOH HOH . H 5 HOH A 65 547 547 HOH HOH . H 5 HOH A 66 548 548 HOH HOH . H 5 HOH A 67 549 549 HOH HOH . H 5 HOH A 68 550 550 HOH HOH . H 5 HOH A 69 551 551 HOH HOH . H 5 HOH A 70 552 552 HOH HOH . H 5 HOH A 71 553 553 HOH HOH . H 5 HOH A 72 554 554 HOH HOH . H 5 HOH A 73 555 555 HOH HOH . H 5 HOH A 74 556 556 HOH HOH . H 5 HOH A 75 557 557 HOH HOH . H 5 HOH A 76 558 558 HOH HOH . H 5 HOH A 77 559 559 HOH HOH . H 5 HOH A 78 560 560 HOH HOH . H 5 HOH A 79 561 561 HOH HOH . H 5 HOH A 80 562 562 HOH HOH . H 5 HOH A 81 563 563 HOH HOH . H 5 HOH A 82 564 564 HOH HOH . H 5 HOH A 83 565 565 HOH HOH . I 5 HOH B 1 484 484 HOH HOH . I 5 HOH B 2 485 485 HOH HOH . I 5 HOH B 3 486 486 HOH HOH . I 5 HOH B 4 487 487 HOH HOH . I 5 HOH B 5 488 488 HOH HOH . I 5 HOH B 6 489 489 HOH HOH . I 5 HOH B 7 490 490 HOH HOH . I 5 HOH B 8 491 491 HOH HOH . I 5 HOH B 9 492 492 HOH HOH . I 5 HOH B 10 493 493 HOH HOH . I 5 HOH B 11 494 494 HOH HOH . I 5 HOH B 12 495 495 HOH HOH . I 5 HOH B 13 496 496 HOH HOH . I 5 HOH B 14 497 497 HOH HOH . I 5 HOH B 15 498 498 HOH HOH . I 5 HOH B 16 499 499 HOH HOH . I 5 HOH B 17 500 500 HOH HOH . I 5 HOH B 18 501 501 HOH HOH . I 5 HOH B 19 502 502 HOH HOH . I 5 HOH B 20 503 503 HOH HOH . I 5 HOH B 21 504 504 HOH HOH . I 5 HOH B 22 505 505 HOH HOH . I 5 HOH B 23 506 506 HOH HOH . I 5 HOH B 24 507 507 HOH HOH . I 5 HOH B 25 508 508 HOH HOH . I 5 HOH B 26 509 509 HOH HOH . I 5 HOH B 27 510 510 HOH HOH . I 5 HOH B 28 511 511 HOH HOH . I 5 HOH B 29 512 512 HOH HOH . I 5 HOH B 30 513 513 HOH HOH . I 5 HOH B 31 514 514 HOH HOH . I 5 HOH B 32 515 515 HOH HOH . I 5 HOH B 33 516 516 HOH HOH . I 5 HOH B 34 517 517 HOH HOH . I 5 HOH B 35 518 518 HOH HOH . I 5 HOH B 36 519 519 HOH HOH . I 5 HOH B 37 520 520 HOH HOH . I 5 HOH B 38 521 521 HOH HOH . I 5 HOH B 39 522 522 HOH HOH . I 5 HOH B 40 523 523 HOH HOH . I 5 HOH B 41 524 524 HOH HOH . I 5 HOH B 42 525 525 HOH HOH . I 5 HOH B 43 526 526 HOH HOH . I 5 HOH B 44 527 527 HOH HOH . I 5 HOH B 45 528 528 HOH HOH . I 5 HOH B 46 529 529 HOH HOH . I 5 HOH B 47 530 530 HOH HOH . I 5 HOH B 48 531 531 HOH HOH . I 5 HOH B 49 532 532 HOH HOH . I 5 HOH B 50 533 533 HOH HOH . I 5 HOH B 51 534 534 HOH HOH . I 5 HOH B 52 535 535 HOH HOH . I 5 HOH B 53 536 536 HOH HOH . I 5 HOH B 54 537 537 HOH HOH . I 5 HOH B 55 538 538 HOH HOH . I 5 HOH B 56 539 539 HOH HOH . I 5 HOH B 57 540 540 HOH HOH . I 5 HOH B 58 541 541 HOH HOH . I 5 HOH B 59 542 542 HOH HOH . I 5 HOH B 60 543 543 HOH HOH . I 5 HOH B 61 544 544 HOH HOH . I 5 HOH B 62 545 545 HOH HOH . I 5 HOH B 63 546 546 HOH HOH . I 5 HOH B 64 547 547 HOH HOH . I 5 HOH B 65 548 548 HOH HOH . I 5 HOH B 66 549 549 HOH HOH . I 5 HOH B 67 550 550 HOH HOH . I 5 HOH B 68 551 551 HOH HOH . I 5 HOH B 69 552 552 HOH HOH . I 5 HOH B 70 553 553 HOH HOH . I 5 HOH B 71 554 554 HOH HOH . I 5 HOH B 72 555 555 HOH HOH . I 5 HOH B 73 556 556 HOH HOH . I 5 HOH B 74 557 557 HOH HOH . I 5 HOH B 75 558 558 HOH HOH . I 5 HOH B 76 559 559 HOH HOH . I 5 HOH B 77 560 560 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 P AMP . . . D 3 -2.62 7.379 -72.261 1 58.45 ? P AMP 482 A 1 HETATM 2 O O1P AMP . . . D 3 -3.162 8.69 -72.803 1 53.43 ? O1P AMP 482 A 1 HETATM 3 O O2P AMP . . . D 3 -1.099 7.163 -72.35 1 53 ? O2P AMP 482 A 1 HETATM 4 O O3P AMP . . . D 3 -3.235 7.019 -70.932 1 57.35 ? O3P AMP 482 A 1 HETATM 5 O O5' AMP . . . D 3 -3.271 6.297 -73.265 1 49.94 ? O5' AMP 482 A 1 HETATM 6 C C5' AMP . . . D 3 -4.65 6.353 -73.605 1 41.88 ? C5' AMP 482 A 1 HETATM 7 C C4' AMP . . . D 3 -5.065 5.034 -74.247 1 39.3 ? C4' AMP 482 A 1 HETATM 8 O O4' AMP . . . D 3 -4.021 4.478 -75.062 1 34.03 ? O4' AMP 482 A 1 HETATM 9 C C3' AMP . . . D 3 -5.411 3.992 -73.185 1 38.7 ? C3' AMP 482 A 1 HETATM 10 O O3' AMP . . . D 3 -6.576 3.244 -73.614 1 37.92 ? O3' AMP 482 A 1 HETATM 11 C C2' AMP . . . D 3 -4.158 3.134 -73.122 1 36.04 ? C2' AMP 482 A 1 HETATM 12 O O2' AMP . . . D 3 -4.389 1.799 -72.665 1 35.06 ? O2' AMP 482 A 1 HETATM 13 C C1' AMP . . . D 3 -3.738 3.159 -74.581 1 34.67 ? C1' AMP 482 A 1 HETATM 14 N N9 AMP . . . D 3 -2.31 2.867 -74.778 1 31.91 ? N9 AMP 482 A 1 HETATM 15 C C8 AMP . . . D 3 -1.268 3.471 -74.181 1 32.5 ? C8 AMP 482 A 1 HETATM 16 N N7 AMP . . . D 3 -0.088 2.95 -74.615 1 31.23 ? N7 AMP 482 A 1 HETATM 17 C C5 AMP . . . D 3 -0.383 1.983 -75.504 1 29.91 ? C5 AMP 482 A 1 HETATM 18 C C6 AMP . . . D 3 0.385 1.036 -76.353 1 27.69 ? C6 AMP 482 A 1 HETATM 19 N N6 AMP . . . D 3 1.731 1.002 -76.35 1 25.71 ? N6 AMP 482 A 1 HETATM 20 N N1 AMP . . . D 3 -0.333 0.197 -77.135 1 28.09 ? N1 AMP 482 A 1 HETATM 21 C C2 AMP . . . D 3 -1.684 0.205 -77.17 1 28.35 ? C2 AMP 482 A 1 HETATM 22 N N3 AMP . . . D 3 -2.455 1.045 -76.429 1 29.15 ? N3 AMP 482 A 1 HETATM 23 C C4 AMP . . . D 3 -1.861 1.939 -75.601 1 30.24 ? C4 AMP 482 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #