data_1KHR # _model_server_result.job_id a4zGCh-pxxz4-wehXzC_3A _model_server_result.datetime_utc '2024-11-29 11:33:44' _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 1khr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":403}' # _entry.id 1KHR # _exptl.entry_id 1KHR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 525.593 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 'VIRGINIAMYCIN M1' _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 90 _cell.angle_gamma 90 _cell.entry_id 1KHR _cell.length_a 186.1 _cell.length_b 185.9 _cell.length_c 186.9 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KHR _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'F 2 2 2' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,H,I,J,K,P,Q,R 1 1 D,E,F,L,M,N,O,S,T,U 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 G N N ? 2 H N N ? 2 M N N # _chem_comp.formula 'C28 H35 N3 O7' _chem_comp.formula_weight 525.593 _chem_comp.id VIR _chem_comp.mon_nstd_flag . _chem_comp.name 'VIRGINIAMYCIN M1' _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 VIR doub 462 n n C1 C37 VIR sing 463 n n C1 N5 VIR sing 464 n n C10 C13 VIR sing 465 n n C10 N9 VIR doub 466 n y C10 O11 VIR sing 467 n y C12 C8 VIR doub 468 n y C12 O11 VIR sing 469 n y C12 H12 VIR sing 470 n n C13 C14 VIR sing 471 n n C13 H131 VIR sing 472 n n C13 H132 VIR sing 473 n n C14 C16 VIR sing 474 n n C14 O15 VIR doub 475 n n C16 C17 VIR sing 476 n n C16 H161 VIR sing 477 n n C16 H162 VIR sing 478 n n C17 C19 VIR sing 479 n n C17 O18 VIR sing 480 n n C17 H17 VIR sing 481 n n C19 C20 VIR doub 482 e n C19 H19 VIR sing 483 n n C2 C3 VIR sing 484 n n C2 HC2 VIR sing 485 n n C20 C21 VIR sing 486 n n C20 C22 VIR sing 487 n n C21 H211 VIR sing 488 n n C21 H212 VIR sing 489 n n C21 H213 VIR sing 490 n n C22 C23 VIR doub 491 e n C22 H22 VIR sing 492 n n C23 C24 VIR sing 493 n n C23 H23 VIR sing 494 n n C24 N25 VIR sing 495 n n C24 H241 VIR sing 496 n n C24 H242 VIR sing 497 n n C26 C28 VIR sing 498 n n C26 N25 VIR sing 499 n n C26 O27 VIR doub 500 n n C28 C29 VIR doub 501 e n C28 H28 VIR sing 502 n n C29 C30 VIR sing 503 n n C29 H29 VIR sing 504 n n C3 C4 VIR sing 505 n n C3 HC31 VIR sing 506 n n C3 HC32 VIR sing 507 n n C30 C31 VIR sing 508 n n C30 C32 VIR sing 509 n n C30 H30 VIR sing 510 n n C31 H311 VIR sing 511 n n C31 H312 VIR sing 512 n n C31 H313 VIR sing 513 n n C32 C33 VIR sing 514 n n C32 O36 VIR sing 515 n n C32 H32 VIR sing 516 n n C33 C34 VIR sing 517 n n C33 C35 VIR sing 518 n n C33 H33 VIR sing 519 n n C34 H341 VIR sing 520 n n C34 H342 VIR sing 521 n n C34 H343 VIR sing 522 n n C35 H351 VIR sing 523 n n C35 H352 VIR sing 524 n n C35 H353 VIR sing 525 n n C37 O36 VIR sing 526 n n C37 O38 VIR doub 527 n n C4 N5 VIR sing 528 n n C4 HC41 VIR sing 529 n n C4 HC42 VIR sing 530 n n C6 C8 VIR sing 531 n n C6 N5 VIR sing 532 n n C6 O7 VIR doub 533 n n C8 N9 VIR sing 534 n y N25 H25 VIR sing 535 n n O18 H18' VIR sing 536 n n # _atom_sites.entry_id 1KHR _atom_sites.fract_transf_matrix[1][1] 0.005373 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005379 _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] 0.00535 _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 G 2 VIR A 1 401 305 VIR VIR . H 2 VIR A 1 402 305 VIR VIR . I 3 COA A 1 301 302 COA COA . J 3 COA B 1 302 302 COA COA . K 3 COA C 1 303 302 COA COA . L 3 COA D 1 304 302 COA COA . M 2 VIR E 1 403 305 VIR VIR . N 3 COA E 1 305 302 COA COA . O 3 COA F 1 306 302 COA COA . P 4 HOH A 1 3514 3514 HOH TIP . P 4 HOH A 2 3519 3519 HOH TIP . P 4 HOH A 3 3520 3520 HOH TIP . P 4 HOH A 4 3523 3523 HOH TIP . P 4 HOH A 5 3526 3526 HOH TIP . P 4 HOH A 6 3533 3533 HOH TIP . P 4 HOH A 7 3550 3550 HOH TIP . P 4 HOH A 8 3559 3559 HOH TIP . P 4 HOH A 9 3583 3583 HOH TIP . P 4 HOH A 10 3584 3584 HOH TIP . P 4 HOH A 11 3603 3603 HOH TIP . P 4 HOH A 12 3607 3607 HOH TIP . P 4 HOH A 13 3608 3608 HOH TIP . P 4 HOH A 14 3611 3611 HOH TIP . P 4 HOH A 15 3623 3623 HOH TIP . Q 4 HOH B 1 3500 3500 HOH TIP . Q 4 HOH B 2 3503 3503 HOH TIP . Q 4 HOH B 3 3504 3504 HOH TIP . Q 4 HOH B 4 3505 3505 HOH TIP . Q 4 HOH B 5 3506 3506 HOH TIP . Q 4 HOH B 6 3507 3507 HOH TIP . Q 4 HOH B 7 3508 3508 HOH TIP . Q 4 HOH B 8 3511 3511 HOH TIP . Q 4 HOH B 9 3534 3534 HOH TIP . Q 4 HOH B 10 3542 3542 HOH TIP . Q 4 HOH B 11 3544 3544 HOH TIP . Q 4 HOH B 12 3546 3546 HOH TIP . Q 4 HOH B 13 3549 3549 HOH TIP . Q 4 HOH B 14 3563 3563 HOH TIP . Q 4 HOH B 15 3568 3568 HOH TIP . Q 4 HOH B 16 3572 3572 HOH TIP . Q 4 HOH B 17 3576 3576 HOH TIP . Q 4 HOH B 18 3577 3577 HOH TIP . Q 4 HOH B 19 3578 3578 HOH TIP . Q 4 HOH B 20 3579 3579 HOH TIP . Q 4 HOH B 21 3585 3585 HOH TIP . Q 4 HOH B 22 3612 3612 HOH TIP . R 4 HOH C 1 3517 3517 HOH TIP . R 4 HOH C 2 3521 3521 HOH TIP . R 4 HOH C 3 3527 3527 HOH TIP . R 4 HOH C 4 3530 3530 HOH TIP . R 4 HOH C 5 3532 3532 HOH TIP . R 4 HOH C 6 3535 3535 HOH TIP . R 4 HOH C 7 3543 3543 HOH TIP . R 4 HOH C 8 3552 3552 HOH TIP . R 4 HOH C 9 3561 3561 HOH TIP . R 4 HOH C 10 3573 3573 HOH TIP . R 4 HOH C 11 3582 3582 HOH TIP . R 4 HOH C 12 3586 3586 HOH TIP . R 4 HOH C 13 3587 3587 HOH TIP . R 4 HOH C 14 3604 3604 HOH TIP . R 4 HOH C 15 3605 3605 HOH TIP . R 4 HOH C 16 3606 3606 HOH TIP . S 4 HOH D 1 3502 3502 HOH TIP . S 4 HOH D 2 3512 3512 HOH TIP . S 4 HOH D 3 3513 3513 HOH TIP . S 4 HOH D 4 3524 3524 HOH TIP . S 4 HOH D 5 3528 3528 HOH TIP . S 4 HOH D 6 3529 3529 HOH TIP . S 4 HOH D 7 3531 3531 HOH TIP . S 4 HOH D 8 3538 3538 HOH TIP . S 4 HOH D 9 3540 3540 HOH TIP . S 4 HOH D 10 3541 3541 HOH TIP . S 4 HOH D 11 3548 3548 HOH TIP . S 4 HOH D 12 3551 3551 HOH TIP . S 4 HOH D 13 3553 3553 HOH TIP . S 4 HOH D 14 3555 3555 HOH TIP . S 4 HOH D 15 3569 3569 HOH TIP . S 4 HOH D 16 3571 3571 HOH TIP . S 4 HOH D 17 3580 3580 HOH TIP . S 4 HOH D 18 3588 3588 HOH TIP . S 4 HOH D 19 3590 3590 HOH TIP . S 4 HOH D 20 3591 3591 HOH TIP . S 4 HOH D 21 3592 3592 HOH TIP . S 4 HOH D 22 3614 3614 HOH TIP . S 4 HOH D 23 3620 3620 HOH TIP . T 4 HOH E 1 3509 3509 HOH TIP . T 4 HOH E 2 3510 3510 HOH TIP . T 4 HOH E 3 3515 3515 HOH TIP . T 4 HOH E 4 3518 3518 HOH TIP . T 4 HOH E 5 3525 3525 HOH TIP . T 4 HOH E 6 3537 3537 HOH TIP . T 4 HOH E 7 3539 3539 HOH TIP . T 4 HOH E 8 3547 3547 HOH TIP . T 4 HOH E 9 3554 3554 HOH TIP . T 4 HOH E 10 3557 3557 HOH TIP . T 4 HOH E 11 3558 3558 HOH TIP . T 4 HOH E 12 3564 3564 HOH TIP . T 4 HOH E 13 3565 3565 HOH TIP . T 4 HOH E 14 3567 3567 HOH TIP . T 4 HOH E 15 3570 3570 HOH TIP . T 4 HOH E 16 3574 3574 HOH TIP . T 4 HOH E 17 3593 3593 HOH TIP . T 4 HOH E 18 3594 3594 HOH TIP . T 4 HOH E 19 3595 3595 HOH TIP . T 4 HOH E 20 3596 3596 HOH TIP . T 4 HOH E 21 3615 3615 HOH TIP . T 4 HOH E 22 3616 3616 HOH TIP . T 4 HOH E 23 3622 3622 HOH TIP . U 4 HOH F 1 3501 3501 HOH TIP . U 4 HOH F 2 3516 3516 HOH TIP . U 4 HOH F 3 3522 3522 HOH TIP . U 4 HOH F 4 3536 3536 HOH TIP . U 4 HOH F 5 3545 3545 HOH TIP . U 4 HOH F 6 3562 3562 HOH TIP . U 4 HOH F 7 3566 3566 HOH TIP . U 4 HOH F 8 3598 3598 HOH TIP . U 4 HOH F 9 3599 3599 HOH TIP . U 4 HOH F 10 3600 3600 HOH TIP . U 4 HOH F 11 3602 3602 HOH TIP . U 4 HOH F 12 3619 3619 HOH TIP . U 4 HOH F 13 3621 3621 HOH TIP . # 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 VIR . . . M 2 -7.359 -41.545 -27.034 0.8 34.39 ? C1 VIR 403 E 1 HETATM 2 C C10 VIR . . . M 2 -11.007 -38.901 -30.535 0.8 38.64 ? C10 VIR 403 E 1 HETATM 3 C C12 VIR . . . M 2 -10.429 -40.896 -31.091 0.8 38.51 ? C12 VIR 403 E 1 HETATM 4 C C13 VIR . . . M 2 -11.693 -37.617 -30.72 0.8 38.75 ? C13 VIR 403 E 1 HETATM 5 C C14 VIR . . . M 2 -11.16 -36.597 -29.814 0.8 37.71 ? C14 VIR 403 E 1 HETATM 6 C C16 VIR . . . M 2 -9.936 -35.859 -30.253 0.8 33.31 ? C16 VIR 403 E 1 HETATM 7 C C17 VIR . . . M 2 -9.233 -35.197 -29.101 0.8 29.46 ? C17 VIR 403 E 1 HETATM 8 C C19 VIR . . . M 2 -7.97 -35.885 -28.671 0.8 24.36 ? C19 VIR 403 E 1 HETATM 9 C C2 VIR . . . M 2 -7.268 -40.878 -25.853 0.8 34.02 ? C2 VIR 403 E 1 HETATM 10 C C20 VIR . . . M 2 -7.626 -36.123 -27.441 0.8 22.84 ? C20 VIR 403 E 1 HETATM 11 C C21 VIR . . . M 2 -8.465 -35.713 -26.257 0.8 22.17 ? C21 VIR 403 E 1 HETATM 12 C C22 VIR . . . M 2 -6.384 -36.839 -27.257 0.8 22.51 ? C22 VIR 403 E 1 HETATM 13 C C23 VIR . . . M 2 -5.748 -36.914 -26.047 0.8 18.24 ? C23 VIR 403 E 1 HETATM 14 C C24 VIR . . . M 2 -4.472 -37.729 -25.866 0.8 17.84 ? C24 VIR 403 E 1 HETATM 15 C C26 VIR . . . M 2 -3.874 -39.982 -26.496 0.8 26.36 ? C26 VIR 403 E 1 HETATM 16 C C28 VIR . . . M 2 -4.587 -41.361 -26.166 0.8 25.71 ? C28 VIR 403 E 1 HETATM 17 C C29 VIR . . . M 2 -4.076 -42.215 -25.632 0.8 28.39 ? C29 VIR 403 E 1 HETATM 18 C C3 VIR . . . M 2 -8.182 -39.674 -25.904 0.8 30.42 ? C3 VIR 403 E 1 HETATM 19 C C30 VIR . . . M 2 -4.442 -43.616 -25.106 0.8 30.39 ? C30 VIR 403 E 1 HETATM 20 C C31 VIR . . . M 2 -5.108 -43.602 -23.711 0.8 29.13 ? C31 VIR 403 E 1 HETATM 21 C C32 VIR . . . M 2 -5.299 -44.418 -26.121 0.8 32.14 ? C32 VIR 403 E 1 HETATM 22 C C33 VIR . . . M 2 -5.686 -45.731 -25.461 0.8 34.62 ? C33 VIR 403 E 1 HETATM 23 C C34 VIR . . . M 2 -6.536 -46.593 -26.402 0.8 37.38 ? C34 VIR 403 E 1 HETATM 24 C C35 VIR . . . M 2 -4.424 -46.528 -25.122 0.8 36.17 ? C35 VIR 403 E 1 HETATM 25 C C37 VIR . . . M 2 -6.626 -42.759 -27.423 0.8 33.19 ? C37 VIR 403 E 1 HETATM 26 C C4 VIR . . . M 2 -8.797 -39.665 -27.283 0.8 30.5 ? C4 VIR 403 E 1 HETATM 27 C C6 VIR . . . M 2 -8.981 -41.522 -28.989 0.8 35.86 ? C6 VIR 403 E 1 HETATM 28 C C8 VIR . . . M 2 -9.872 -40.596 -29.858 0.8 36.61 ? C8 VIR 403 E 1 HETATM 29 N N25 VIR . . . M 2 -4.693 -39.146 -25.872 0.8 23.56 ? N25 VIR 403 E 1 HETATM 30 N N5 VIR . . . M 2 -8.284 -40.9 -27.965 0.8 32.84 ? N5 VIR 403 E 1 HETATM 31 N N9 VIR . . . M 2 -10.281 -39.313 -29.547 0.8 37.7 ? N9 VIR 403 E 1 HETATM 32 O O11 VIR . . . M 2 -11.16 -39.826 -31.513 0.8 38.32 ? O11 VIR 403 E 1 HETATM 33 O O15 VIR . . . M 2 -11.719 -36.375 -28.733 0.8 39.95 ? O15 VIR 403 E 1 HETATM 34 O O18 VIR . . . M 2 -8.888 -33.853 -29.517 0.8 29.36 ? O18 VIR 403 E 1 HETATM 35 O O27 VIR . . . M 2 -2.86 -39.607 -27.137 0.8 29.09 ? O27 VIR 403 E 1 HETATM 36 O O36 VIR . . . M 2 -6.576 -43.681 -26.394 0.8 34.71 ? O36 VIR 403 E 1 HETATM 37 O O38 VIR . . . M 2 -6.13 -42.904 -28.519 0.8 37.28 ? O38 VIR 403 E 1 HETATM 38 O O7 VIR . . . M 2 -8.929 -42.712 -29.243 0.8 34.94 ? O7 VIR 403 E 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 38 #