data_3QBI # _model_server_result.job_id xC52r9HVLa6S34qO7TqRug _model_server_result.datetime_utc '2024-11-02 13:39:17' _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 3qbi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":292}' # _entry.id 3QBI # _exptl.entry_id 3QBI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 128.68 _cell.angle_gamma 90 _cell.entry_id 3QBI _cell.length_a 153.96 _cell.length_b 97.97 _cell.length_c 100.65 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QBI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,L,M,N,O _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 ? 2 D N N ? 2 H N N ? 2 K 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 NZ LYS 256 A LYS 256 1_555 D C15 RET . A RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale2 B NZ LYS 256 B LYS 256 1_555 H C15 RET . B RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale3 C NZ LYS 256 D LYS 256 1_555 K C15 RET . D RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _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 C1 C2 RET sing 457 n n C1 C6 RET sing 458 n n C1 C16 RET sing 459 n n C1 C17 RET sing 460 n n C2 C3 RET sing 461 n n C2 H21 RET sing 462 n n C2 H22 RET sing 463 n n C3 C4 RET sing 464 n n C3 H31 RET sing 465 n n C3 H32 RET sing 466 n n C4 C5 RET sing 467 n n C4 H41 RET sing 468 n n C4 H42 RET sing 469 n n C5 C6 RET doub 470 n n C5 C18 RET sing 471 n n C6 C7 RET sing 472 n n C7 C8 RET doub 473 e n C7 H7 RET sing 474 n n C8 C9 RET sing 475 n n C8 H8 RET sing 476 n n C9 C10 RET doub 477 e n C9 C19 RET sing 478 n n C10 C11 RET sing 479 n n C10 H10 RET sing 480 n n C11 C12 RET doub 481 e n C11 H11 RET sing 482 n n C12 C13 RET sing 483 n n C12 H12 RET sing 484 n n C13 C14 RET doub 485 e n C13 C20 RET sing 486 n n C14 C15 RET sing 487 n n C14 H14 RET sing 488 n n C15 O1 RET doub 489 n n C15 H15 RET sing 490 n n C16 H161 RET sing 491 n n C16 H162 RET sing 492 n n C16 H163 RET sing 493 n n C17 H171 RET sing 494 n n C17 H172 RET sing 495 n n C17 H173 RET sing 496 n n C18 H181 RET sing 497 n n C18 H182 RET sing 498 n n C18 H183 RET sing 499 n n C19 H191 RET sing 500 n n C19 H192 RET sing 501 n n C19 H193 RET sing 502 n n C20 H201 RET sing 503 n n C20 H202 RET sing 504 n n C20 H203 RET sing 505 n n # _atom_sites.entry_id 3QBI _atom_sites.fract_transf_matrix[1][1] 0.006495 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0052 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010207 _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] 0.012727 _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 D 2 RET A 1 292 292 RET RET . E 3 BNG A 1 403 403 BNG BNG . F 3 BNG A 1 404 404 BNG BNG . G 3 BNG A 1 405 405 BNG BNG . H 2 RET B 1 292 292 RET RET . I 4 22B B 1 300 300 22B 22B . J 3 BNG B 1 402 402 BNG BNG . K 2 RET D 1 292 292 RET RET . L 4 22B D 1 300 300 22B 22B . M 5 HOH A 1 501 501 HOH HOH . M 5 HOH A 2 502 502 HOH HOH . M 5 HOH A 3 503 503 HOH HOH . M 5 HOH A 4 504 504 HOH HOH . M 5 HOH A 5 505 505 HOH HOH . M 5 HOH A 6 506 506 HOH HOH . M 5 HOH A 7 507 507 HOH HOH . M 5 HOH A 8 508 508 HOH HOH . M 5 HOH A 9 509 509 HOH HOH . M 5 HOH A 10 510 510 HOH HOH . M 5 HOH A 11 511 511 HOH HOH . M 5 HOH A 12 512 512 HOH HOH . M 5 HOH A 13 513 513 HOH HOH . M 5 HOH A 14 514 514 HOH HOH . M 5 HOH A 15 515 515 HOH HOH . M 5 HOH A 16 516 516 HOH HOH . M 5 HOH A 17 517 517 HOH HOH . M 5 HOH A 18 518 518 HOH HOH . M 5 HOH A 19 519 519 HOH HOH . M 5 HOH A 20 520 520 HOH HOH . M 5 HOH A 21 521 521 HOH HOH . M 5 HOH A 22 523 523 HOH HOH . M 5 HOH A 23 524 524 HOH HOH . M 5 HOH A 24 525 525 HOH HOH . M 5 HOH A 25 526 526 HOH HOH . M 5 HOH A 26 527 527 HOH HOH . M 5 HOH A 27 529 529 HOH HOH . M 5 HOH A 28 530 530 HOH HOH . M 5 HOH A 29 531 531 HOH HOH . M 5 HOH A 30 533 533 HOH HOH . M 5 HOH A 31 534 534 HOH HOH . M 5 HOH A 32 535 535 HOH HOH . M 5 HOH A 33 537 537 HOH HOH . M 5 HOH A 34 538 538 HOH HOH . M 5 HOH A 35 539 539 HOH HOH . M 5 HOH A 36 540 540 HOH HOH . M 5 HOH A 37 541 541 HOH HOH . M 5 HOH A 38 542 542 HOH HOH . M 5 HOH A 39 543 543 HOH HOH . M 5 HOH A 40 545 545 HOH HOH . M 5 HOH A 41 546 546 HOH HOH . M 5 HOH A 42 547 547 HOH HOH . M 5 HOH A 43 549 549 HOH HOH . M 5 HOH A 44 552 552 HOH HOH . M 5 HOH A 45 554 554 HOH HOH . M 5 HOH A 46 555 555 HOH HOH . M 5 HOH A 47 556 556 HOH HOH . M 5 HOH A 48 557 557 HOH HOH . M 5 HOH A 49 558 558 HOH HOH . M 5 HOH A 50 559 559 HOH HOH . M 5 HOH A 51 560 560 HOH HOH . M 5 HOH A 52 561 561 HOH HOH . M 5 HOH A 53 563 563 HOH HOH . M 5 HOH A 54 564 564 HOH HOH . M 5 HOH A 55 565 565 HOH HOH . M 5 HOH A 56 566 566 HOH HOH . M 5 HOH A 57 567 567 HOH HOH . M 5 HOH A 58 568 568 HOH HOH . M 5 HOH A 59 572 572 HOH HOH . M 5 HOH A 60 573 573 HOH HOH . M 5 HOH A 61 574 574 HOH HOH . M 5 HOH A 62 577 577 HOH HOH . M 5 HOH A 63 600 600 HOH HOH . M 5 HOH A 64 601 601 HOH HOH . M 5 HOH A 65 602 602 HOH HOH . N 5 HOH B 1 501 501 HOH HOH . N 5 HOH B 2 503 503 HOH HOH . N 5 HOH B 3 504 504 HOH HOH . N 5 HOH B 4 505 505 HOH HOH . N 5 HOH B 5 506 506 HOH HOH . N 5 HOH B 6 507 507 HOH HOH . N 5 HOH B 7 508 508 HOH HOH . N 5 HOH B 8 509 509 HOH HOH . N 5 HOH B 9 510 510 HOH HOH . N 5 HOH B 10 511 511 HOH HOH . N 5 HOH B 11 512 512 HOH HOH . N 5 HOH B 12 513 513 HOH HOH . N 5 HOH B 13 515 515 HOH HOH . N 5 HOH B 14 516 516 HOH HOH . N 5 HOH B 15 517 517 HOH HOH . N 5 HOH B 16 518 518 HOH HOH . N 5 HOH B 17 519 519 HOH HOH . N 5 HOH B 18 520 520 HOH HOH . N 5 HOH B 19 521 521 HOH HOH . N 5 HOH B 20 523 523 HOH HOH . N 5 HOH B 21 524 524 HOH HOH . N 5 HOH B 22 526 526 HOH HOH . N 5 HOH B 23 531 531 HOH HOH . N 5 HOH B 24 533 533 HOH HOH . N 5 HOH B 25 534 534 HOH HOH . N 5 HOH B 26 535 535 HOH HOH . N 5 HOH B 27 536 536 HOH HOH . N 5 HOH B 28 537 537 HOH HOH . N 5 HOH B 29 538 538 HOH HOH . N 5 HOH B 30 539 539 HOH HOH . N 5 HOH B 31 540 540 HOH HOH . N 5 HOH B 32 541 541 HOH HOH . N 5 HOH B 33 542 542 HOH HOH . N 5 HOH B 34 543 543 HOH HOH . N 5 HOH B 35 544 544 HOH HOH . N 5 HOH B 36 545 545 HOH HOH . N 5 HOH B 37 546 546 HOH HOH . N 5 HOH B 38 547 547 HOH HOH . N 5 HOH B 39 549 549 HOH HOH . N 5 HOH B 40 551 551 HOH HOH . N 5 HOH B 41 552 552 HOH HOH . N 5 HOH B 42 553 553 HOH HOH . N 5 HOH B 43 554 554 HOH HOH . N 5 HOH B 44 555 555 HOH HOH . N 5 HOH B 45 556 556 HOH HOH . N 5 HOH B 46 557 557 HOH HOH . N 5 HOH B 47 558 558 HOH HOH . N 5 HOH B 48 559 559 HOH HOH . N 5 HOH B 49 560 560 HOH HOH . N 5 HOH B 50 561 561 HOH HOH . N 5 HOH B 51 562 562 HOH HOH . N 5 HOH B 52 563 563 HOH HOH . N 5 HOH B 53 564 564 HOH HOH . N 5 HOH B 54 565 565 HOH HOH . N 5 HOH B 55 566 566 HOH HOH . N 5 HOH B 56 567 567 HOH HOH . N 5 HOH B 57 569 569 HOH HOH . N 5 HOH B 58 570 570 HOH HOH . N 5 HOH B 59 571 571 HOH HOH . N 5 HOH B 60 573 573 HOH HOH . N 5 HOH B 61 575 575 HOH HOH . N 5 HOH B 62 576 576 HOH HOH . N 5 HOH B 63 578 578 HOH HOH . N 5 HOH B 64 600 600 HOH HOH . N 5 HOH B 65 601 601 HOH HOH . N 5 HOH B 66 602 602 HOH HOH . N 5 HOH B 67 603 603 HOH HOH . N 5 HOH B 68 604 604 HOH HOH . N 5 HOH B 69 605 605 HOH HOH . N 5 HOH B 70 606 606 HOH HOH . N 5 HOH B 71 607 607 HOH HOH . N 5 HOH B 72 608 608 HOH HOH . N 5 HOH B 73 609 609 HOH HOH . N 5 HOH B 74 610 610 HOH HOH . N 5 HOH B 75 611 611 HOH HOH . O 5 HOH D 1 501 501 HOH HOH . O 5 HOH D 2 503 503 HOH HOH . O 5 HOH D 3 504 504 HOH HOH . O 5 HOH D 4 505 505 HOH HOH . O 5 HOH D 5 506 506 HOH HOH . O 5 HOH D 6 507 507 HOH HOH . O 5 HOH D 7 508 508 HOH HOH . O 5 HOH D 8 509 509 HOH HOH . O 5 HOH D 9 510 510 HOH HOH . O 5 HOH D 10 511 511 HOH HOH . O 5 HOH D 11 512 512 HOH HOH . O 5 HOH D 12 513 513 HOH HOH . O 5 HOH D 13 515 515 HOH HOH . O 5 HOH D 14 516 516 HOH HOH . O 5 HOH D 15 517 517 HOH HOH . O 5 HOH D 16 518 518 HOH HOH . O 5 HOH D 17 519 519 HOH HOH . O 5 HOH D 18 520 520 HOH HOH . O 5 HOH D 19 523 523 HOH HOH . O 5 HOH D 20 524 524 HOH HOH . O 5 HOH D 21 525 525 HOH HOH . O 5 HOH D 22 533 533 HOH HOH . O 5 HOH D 23 534 534 HOH HOH . O 5 HOH D 24 535 535 HOH HOH . O 5 HOH D 25 537 537 HOH HOH . O 5 HOH D 26 539 539 HOH HOH . O 5 HOH D 27 541 541 HOH HOH . O 5 HOH D 28 542 542 HOH HOH . O 5 HOH D 29 543 543 HOH HOH . O 5 HOH D 30 545 545 HOH HOH . O 5 HOH D 31 546 546 HOH HOH . O 5 HOH D 32 547 547 HOH HOH . O 5 HOH D 33 548 548 HOH HOH . O 5 HOH D 34 549 549 HOH HOH . O 5 HOH D 35 550 550 HOH HOH . O 5 HOH D 36 552 552 HOH HOH . O 5 HOH D 37 553 553 HOH HOH . O 5 HOH D 38 554 554 HOH HOH . O 5 HOH D 39 555 555 HOH HOH . O 5 HOH D 40 556 556 HOH HOH . O 5 HOH D 41 557 557 HOH HOH . O 5 HOH D 42 558 558 HOH HOH . O 5 HOH D 43 559 559 HOH HOH . O 5 HOH D 44 560 560 HOH HOH . O 5 HOH D 45 561 561 HOH HOH . O 5 HOH D 46 562 562 HOH HOH . O 5 HOH D 47 563 563 HOH HOH . O 5 HOH D 48 564 564 HOH HOH . O 5 HOH D 49 565 565 HOH HOH . O 5 HOH D 50 566 566 HOH HOH . O 5 HOH D 51 567 567 HOH HOH . O 5 HOH D 52 568 568 HOH HOH . O 5 HOH D 53 569 569 HOH HOH . O 5 HOH D 54 570 570 HOH HOH . O 5 HOH D 55 571 571 HOH HOH . O 5 HOH D 56 572 572 HOH HOH . O 5 HOH D 57 575 575 HOH HOH . O 5 HOH D 58 576 576 HOH HOH . O 5 HOH D 59 577 577 HOH HOH . O 5 HOH D 60 578 578 HOH HOH . O 5 HOH D 61 579 579 HOH HOH . O 5 HOH D 62 580 580 HOH HOH . O 5 HOH D 63 581 581 HOH HOH . O 5 HOH D 64 582 582 HOH HOH . O 5 HOH D 65 583 583 HOH HOH . O 5 HOH D 66 584 584 HOH HOH . O 5 HOH D 67 585 585 HOH HOH . O 5 HOH D 68 586 586 HOH HOH . O 5 HOH D 69 600 600 HOH HOH . O 5 HOH D 70 601 601 HOH HOH . O 5 HOH D 71 602 602 HOH HOH . O 5 HOH D 72 612 612 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 C C1 RET . . . D 2 40.685 -5.657 22.381 1 17.84 ? C1 RET 292 A 1 HETATM 2 C C2 RET . . . D 2 41.151 -6.719 21.298 1 18.02 ? C2 RET 292 A 1 HETATM 3 C C3 RET . . . D 2 41.606 -6.237 20.004 1 19.55 ? C3 RET 292 A 1 HETATM 4 C C4 RET . . . D 2 42.567 -5.062 20.069 1 16.6 ? C4 RET 292 A 1 HETATM 5 C C5 RET . . . D 2 42.241 -3.995 21.111 1 16.07 ? C5 RET 292 A 1 HETATM 6 C C6 RET . . . D 2 41.377 -4.205 22.204 1 15.88 ? C6 RET 292 A 1 HETATM 7 C C7 RET . . . D 2 41.162 -3.025 23.18 1 17.23 ? C7 RET 292 A 1 HETATM 8 C C8 RET . . . D 2 40.361 -2.952 24.27 1 15 ? C8 RET 292 A 1 HETATM 9 C C9 RET . . . D 2 40.292 -1.889 25.262 1 18.02 ? C9 RET 292 A 1 HETATM 10 C C10 RET . . . D 2 39.357 -2.062 26.25 1 17.22 ? C10 RET 292 A 1 HETATM 11 C C11 RET . . . D 2 39.104 -1.223 27.403 1 22.08 ? C11 RET 292 A 1 HETATM 12 C C12 RET . . . D 2 38.132 -1.549 28.259 1 19.99 ? C12 RET 292 A 1 HETATM 13 C C13 RET . . . D 2 37.747 -0.814 29.475 1 21.25 ? C13 RET 292 A 1 HETATM 14 C C14 RET . . . D 2 36.629 -1.292 30.074 1 20.47 ? C14 RET 292 A 1 HETATM 15 C C15 RET . . . D 2 35.833 -0.789 31.176 1 20.83 ? C15 RET 292 A 1 HETATM 16 C C16 RET . . . D 2 39.162 -5.603 22.182 1 15.29 ? C16 RET 292 A 1 HETATM 17 C C17 RET . . . D 2 40.992 -6.332 23.731 1 15 ? C17 RET 292 A 1 HETATM 18 C C18 RET . . . D 2 42.988 -2.7 20.804 1 18.1 ? C18 RET 292 A 1 HETATM 19 C C19 RET . . . D 2 41.229 -0.702 25.2 1 15 ? C19 RET 292 A 1 HETATM 20 C C20 RET . . . D 2 38.478 0.43 29.941 1 20.04 ? C20 RET 292 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #