data_4XSR # _model_server_result.job_id XcB6Ik2skIVhzrCqL8i0rw _model_server_result.datetime_utc '2024-11-22 11:37:32' _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 4xsr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":405}' # _entry.id 4XSR # _exptl.entry_id 4XSR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 4XSR _cell.length_a 130.228 _cell.length_b 130.228 _cell.length_c 157.359 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XSR _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 4 E N N ? 4 J N N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 395 n n N1 C6 UPG sing 396 n n N1 C1C UPG sing 397 n n C2 N3 UPG sing 398 n n C2 O2 UPG doub 399 n n N3 C4 UPG sing 400 n n N3 HN3 UPG sing 401 n n C4 C5 UPG sing 402 n n C4 O4 UPG doub 403 n n C5 C6 UPG doub 404 n n C5 H5 UPG sing 405 n n C6 H6 UPG sing 406 n n C1C C2C UPG sing 407 n n C1C O4C UPG sing 408 n n C1C H1C UPG sing 409 n n C2C O2C UPG sing 410 n n C2C C3C UPG sing 411 n n C2C H2C UPG sing 412 n n O2C HO2C UPG sing 413 n n C3C C4C UPG sing 414 n n C3C O3C UPG sing 415 n n C3C H3C UPG sing 416 n n C4C O4C UPG sing 417 n n C4C C5C UPG sing 418 n n C4C H4C UPG sing 419 n n O3C HO3C UPG sing 420 n n C5C O5C UPG sing 421 n n C5C H5C1 UPG sing 422 n n C5C H5C2 UPG sing 423 n n O5C PA UPG sing 424 n n PA O1A UPG doub 425 n n PA O2A UPG sing 426 n n PA O3A UPG sing 427 n n O2A HOA2 UPG sing 428 n n O3A PB UPG sing 429 n n PB O1B UPG doub 430 n n PB O2B UPG sing 431 n n PB O3B UPG sing 432 n n O2B HOB2 UPG sing 433 n n O3B C1' UPG sing 434 n n C1' C2' UPG sing 435 n n C1' O5' UPG sing 436 n n C1' H1' UPG sing 437 n n C2' C3' UPG sing 438 n n C2' O2' UPG sing 439 n n C2' H2' UPG sing 440 n n C3' C4' UPG sing 441 n n C3' O3' UPG sing 442 n n C3' H3' UPG sing 443 n n C4' C5' UPG sing 444 n n C4' O4' UPG sing 445 n n C4' H4' UPG sing 446 n n C5' C6' UPG sing 447 n n C5' O5' UPG sing 448 n n C5' H5' UPG sing 449 n n C6' O6' UPG sing 450 n n C6' "H6'1" UPG sing 451 n n C6' "H6'2" UPG sing 452 n n O2' HO2' UPG sing 453 n n O3' HO3' UPG sing 454 n n O4' HO4' UPG sing 455 n n O6' HO6' UPG sing 456 n n # _atom_sites.entry_id 4XSR _atom_sites.fract_transf_matrix[1][1] 0.007679 _atom_sites.fract_transf_matrix[1][2] 0.004433 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008867 _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] 0.006355 _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 EPE B 1 401 401 EPE EPE . D 3 SO4 B 1 402 403 SO4 SO4 . E 4 UPG B 1 403 404 UPG UPG . F 3 SO4 A 1 401 402 SO4 SO4 . G 3 SO4 A 1 402 401 SO4 SO4 . H 2 EPE A 1 403 402 EPE EPE . I 3 SO4 A 1 404 403 SO4 SO4 . J 4 UPG A 1 405 404 UPG UPG . K 5 HOH B 1 501 598 HOH HOH . K 5 HOH B 2 502 568 HOH HOH . K 5 HOH B 3 503 552 HOH HOH . K 5 HOH B 4 504 523 HOH HOH . K 5 HOH B 5 505 525 HOH HOH . K 5 HOH B 6 506 583 HOH HOH . K 5 HOH B 7 507 502 HOH HOH . K 5 HOH B 8 508 580 HOH HOH . K 5 HOH B 9 509 538 HOH HOH . K 5 HOH B 10 510 572 HOH HOH . K 5 HOH B 11 511 577 HOH HOH . K 5 HOH B 12 512 544 HOH HOH . K 5 HOH B 13 513 504 HOH HOH . K 5 HOH B 14 514 550 HOH HOH . K 5 HOH B 15 515 532 HOH HOH . K 5 HOH B 16 516 529 HOH HOH . K 5 HOH B 17 517 591 HOH HOH . K 5 HOH B 18 518 588 HOH HOH . K 5 HOH B 19 519 593 HOH HOH . K 5 HOH B 20 520 501 HOH HOH . K 5 HOH B 21 521 549 HOH HOH . K 5 HOH B 22 522 505 HOH HOH . K 5 HOH B 23 523 594 HOH HOH . K 5 HOH B 24 524 528 HOH HOH . K 5 HOH B 25 525 508 HOH HOH . K 5 HOH B 26 526 560 HOH HOH . K 5 HOH B 27 527 573 HOH HOH . K 5 HOH B 28 528 589 HOH HOH . K 5 HOH B 29 529 579 HOH HOH . K 5 HOH B 30 530 507 HOH HOH . K 5 HOH B 31 531 562 HOH HOH . K 5 HOH B 32 532 561 HOH HOH . K 5 HOH B 33 533 590 HOH HOH . K 5 HOH B 34 534 584 HOH HOH . K 5 HOH B 35 535 503 HOH HOH . K 5 HOH B 36 536 571 HOH HOH . K 5 HOH B 37 537 524 HOH HOH . K 5 HOH B 38 538 2 HOH HOH . K 5 HOH B 39 539 520 HOH HOH . K 5 HOH B 40 540 567 HOH HOH . K 5 HOH B 41 541 521 HOH HOH . K 5 HOH B 42 542 526 HOH HOH . K 5 HOH B 43 543 540 HOH HOH . K 5 HOH B 44 544 575 HOH HOH . K 5 HOH B 45 545 530 HOH HOH . K 5 HOH B 46 546 574 HOH HOH . K 5 HOH B 47 547 586 HOH HOH . K 5 HOH B 48 548 578 HOH HOH . K 5 HOH B 49 549 566 HOH HOH . K 5 HOH B 50 550 551 HOH HOH . K 5 HOH B 51 551 519 HOH HOH . K 5 HOH B 52 552 518 HOH HOH . K 5 HOH B 53 553 570 HOH HOH . K 5 HOH B 54 554 581 HOH HOH . K 5 HOH B 55 555 517 HOH HOH . K 5 HOH B 56 556 563 HOH HOH . K 5 HOH B 57 557 527 HOH HOH . K 5 HOH B 58 558 601 HOH HOH . K 5 HOH B 59 559 600 HOH HOH . K 5 HOH B 60 560 516 HOH HOH . K 5 HOH B 61 561 539 HOH HOH . K 5 HOH B 62 562 585 HOH HOH . K 5 HOH B 63 563 592 HOH HOH . K 5 HOH B 64 564 522 HOH HOH . K 5 HOH B 65 565 510 HOH HOH . K 5 HOH B 66 566 543 HOH HOH . K 5 HOH B 67 567 556 HOH HOH . K 5 HOH B 68 568 564 HOH HOH . K 5 HOH B 69 569 533 HOH HOH . K 5 HOH B 70 570 569 HOH HOH . K 5 HOH B 71 571 565 HOH HOH . K 5 HOH B 72 572 511 HOH HOH . K 5 HOH B 73 573 545 HOH HOH . K 5 HOH B 74 574 531 HOH HOH . K 5 HOH B 75 575 595 HOH HOH . K 5 HOH B 76 576 597 HOH HOH . K 5 HOH B 77 577 555 HOH HOH . K 5 HOH B 78 578 587 HOH HOH . K 5 HOH B 79 579 542 HOH HOH . K 5 HOH B 80 580 558 HOH HOH . K 5 HOH B 81 581 546 HOH HOH . K 5 HOH B 82 582 534 HOH HOH . K 5 HOH B 83 583 553 HOH HOH . K 5 HOH B 84 584 1 HOH HOH . K 5 HOH B 85 585 512 HOH HOH . K 5 HOH B 86 586 513 HOH HOH . K 5 HOH B 87 587 596 HOH HOH . K 5 HOH B 88 588 576 HOH HOH . K 5 HOH B 89 589 3 HOH HOH . K 5 HOH B 90 590 547 HOH HOH . K 5 HOH B 91 591 554 HOH HOH . K 5 HOH B 92 592 548 HOH HOH . K 5 HOH B 93 593 515 HOH HOH . K 5 HOH B 94 594 582 HOH HOH . K 5 HOH B 95 595 557 HOH HOH . L 5 HOH A 1 501 501 HOH HOH . L 5 HOH A 2 502 541 HOH HOH . L 5 HOH A 3 503 563 HOH HOH . L 5 HOH A 4 504 569 HOH HOH . L 5 HOH A 5 505 553 HOH HOH . L 5 HOH A 6 506 532 HOH HOH . L 5 HOH A 7 507 503 HOH HOH . L 5 HOH A 8 508 502 HOH HOH . L 5 HOH A 9 509 542 HOH HOH . L 5 HOH A 10 510 540 HOH HOH . L 5 HOH A 11 511 579 HOH HOH . L 5 HOH A 12 512 527 HOH HOH . L 5 HOH A 13 513 505 HOH HOH . L 5 HOH A 14 514 524 HOH HOH . L 5 HOH A 15 515 520 HOH HOH . L 5 HOH A 16 516 576 HOH HOH . L 5 HOH A 17 517 589 HOH HOH . L 5 HOH A 18 518 567 HOH HOH . L 5 HOH A 19 519 549 HOH HOH . L 5 HOH A 20 520 504 HOH HOH . L 5 HOH A 21 521 571 HOH HOH . L 5 HOH A 22 522 523 HOH HOH . L 5 HOH A 23 523 529 HOH HOH . L 5 HOH A 24 524 581 HOH HOH . L 5 HOH A 25 525 508 HOH HOH . L 5 HOH A 26 526 522 HOH HOH . L 5 HOH A 27 527 562 HOH HOH . L 5 HOH A 28 528 550 HOH HOH . L 5 HOH A 29 529 552 HOH HOH . L 5 HOH A 30 530 572 HOH HOH . L 5 HOH A 31 531 521 HOH HOH . L 5 HOH A 32 532 586 HOH HOH . L 5 HOH A 33 533 587 HOH HOH . L 5 HOH A 34 534 518 HOH HOH . L 5 HOH A 35 535 506 HOH HOH . L 5 HOH A 36 536 574 HOH HOH . L 5 HOH A 37 537 513 HOH HOH . L 5 HOH A 38 538 588 HOH HOH . L 5 HOH A 39 539 596 HOH HOH . L 5 HOH A 40 540 516 HOH HOH . L 5 HOH A 41 541 507 HOH HOH . L 5 HOH A 42 542 515 HOH HOH . L 5 HOH A 43 543 554 HOH HOH . L 5 HOH A 44 544 590 HOH HOH . L 5 HOH A 45 545 7 HOH HOH . L 5 HOH A 46 546 566 HOH HOH . L 5 HOH A 47 547 535 HOH HOH . L 5 HOH A 48 548 537 HOH HOH . L 5 HOH A 49 549 560 HOH HOH . L 5 HOH A 50 550 583 HOH HOH . L 5 HOH A 51 551 510 HOH HOH . L 5 HOH A 52 552 514 HOH HOH . L 5 HOH A 53 553 555 HOH HOH . L 5 HOH A 54 554 533 HOH HOH . L 5 HOH A 55 555 517 HOH HOH . L 5 HOH A 56 556 539 HOH HOH . L 5 HOH A 57 557 536 HOH HOH . L 5 HOH A 58 558 561 HOH HOH . L 5 HOH A 59 559 584 HOH HOH . L 5 HOH A 60 560 509 HOH HOH . L 5 HOH A 61 561 509 HOH HOH . L 5 HOH A 62 562 585 HOH HOH . L 5 HOH A 63 563 578 HOH HOH . L 5 HOH A 64 564 531 HOH HOH . L 5 HOH A 65 565 580 HOH HOH . L 5 HOH A 66 566 565 HOH HOH . L 5 HOH A 67 567 558 HOH HOH . L 5 HOH A 68 568 591 HOH HOH . L 5 HOH A 69 569 525 HOH HOH . L 5 HOH A 70 570 575 HOH HOH . L 5 HOH A 71 571 519 HOH HOH . L 5 HOH A 72 572 534 HOH HOH . L 5 HOH A 73 573 546 HOH HOH . L 5 HOH A 74 574 594 HOH HOH . L 5 HOH A 75 575 548 HOH HOH . L 5 HOH A 76 576 595 HOH HOH . L 5 HOH A 77 577 5 HOH HOH . L 5 HOH A 78 578 528 HOH HOH . L 5 HOH A 79 579 511 HOH HOH . L 5 HOH A 80 580 545 HOH HOH . L 5 HOH A 81 581 568 HOH HOH . L 5 HOH A 82 582 573 HOH HOH . L 5 HOH A 83 583 564 HOH HOH . L 5 HOH A 84 584 577 HOH HOH . L 5 HOH A 85 585 570 HOH HOH . L 5 HOH A 86 586 4 HOH HOH . L 5 HOH A 87 587 556 HOH HOH . L 5 HOH A 88 588 582 HOH HOH . L 5 HOH A 89 589 8 HOH HOH . L 5 HOH A 90 590 593 HOH HOH . L 5 HOH A 91 591 559 HOH HOH . L 5 HOH A 92 592 526 HOH HOH . L 5 HOH A 93 593 538 HOH HOH . L 5 HOH A 94 594 512 HOH HOH . L 5 HOH A 95 595 514 HOH HOH . L 5 HOH A 96 596 592 HOH HOH . L 5 HOH A 97 597 6 HOH HOH . L 5 HOH A 98 598 557 HOH HOH . L 5 HOH A 99 599 544 HOH HOH . L 5 HOH A 100 600 551 HOH HOH . L 5 HOH A 101 601 9 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 N N1 UPG . . . J 4 76.444 -21.9 12.868 1 35.57 ? N1 UPG 405 A 1 HETATM 2 C C2 UPG . . . J 4 76.812 -21.877 14.22 1 33.38 ? C2 UPG 405 A 1 HETATM 3 N N3 UPG . . . J 4 77.98 -22.397 14.571 1 33.45 ? N3 UPG 405 A 1 HETATM 4 C C4 UPG . . . J 4 78.814 -22.927 13.679 1 38.23 ? C4 UPG 405 A 1 HETATM 5 C C5 UPG . . . J 4 78.478 -22.936 12.32 1 36.42 ? C5 UPG 405 A 1 HETATM 6 C C6 UPG . . . J 4 77.26 -22.42 11.941 1 34.62 ? C6 UPG 405 A 1 HETATM 7 O O2 UPG . . . J 4 76.061 -21.392 15.115 1 36.68 ? O2 UPG 405 A 1 HETATM 8 O O4 UPG . . . J 4 79.914 -23.409 14.07 1 37.87 ? O4 UPG 405 A 1 HETATM 9 C C1C UPG . . . J 4 75.161 -21.353 12.442 1 38.78 ? C1C UPG 405 A 1 HETATM 10 C C2C UPG . . . J 4 75.285 -20.235 11.414 1 40.23 ? C2C UPG 405 A 1 HETATM 11 O O2C UPG . . . J 4 75.52 -18.973 12.075 1 38.52 ? O2C UPG 405 A 1 HETATM 12 C C3C UPG . . . J 4 73.932 -20.38 10.72 1 39.4 ? C3C UPG 405 A 1 HETATM 13 C C4C UPG . . . J 4 73.602 -21.886 10.783 1 40.33 ? C4C UPG 405 A 1 HETATM 14 O O4C UPG . . . J 4 74.457 -22.41 11.78 1 40.85 ? O4C UPG 405 A 1 HETATM 15 O O3C UPG . . . J 4 72.96 -19.646 11.468 1 35.14 ? O3C UPG 405 A 1 HETATM 16 C C5C UPG . . . J 4 73.838 -22.69 9.498 1 38.43 ? C5C UPG 405 A 1 HETATM 17 O O5C UPG . . . J 4 72.814 -22.249 8.608 1 39.25 ? O5C UPG 405 A 1 HETATM 18 P PA UPG . . . J 4 72.522 -22.913 7.196 1 36.74 ? PA UPG 405 A 1 HETATM 19 O O1A UPG . . . J 4 71.609 -21.972 6.478 1 36.81 ? O1A UPG 405 A 1 HETATM 20 O O2A UPG . . . J 4 73.741 -23.486 6.566 1 34.12 ? O2A UPG 405 A 1 HETATM 21 O O3A UPG . . . J 4 71.518 -24.092 7.781 1 41.16 ? O3A UPG 405 A 1 HETATM 22 P PB UPG . . . J 4 71.289 -25.623 7.27 1 37.02 ? PB UPG 405 A 1 HETATM 23 O O1B UPG . . . J 4 71.817 -26.43 8.399 1 43.59 ? O1B UPG 405 A 1 HETATM 24 O O2B UPG . . . J 4 71.843 -25.944 5.937 1 34.67 ? O2B UPG 405 A 1 HETATM 25 O O3B UPG . . . J 4 69.672 -25.593 7.395 1 36.22 ? O3B UPG 405 A 1 HETATM 26 C C1' UPG . . . J 4 68.588 -25.581 6.446 1 34.18 ? C1' UPG 405 A 1 HETATM 27 C C2' UPG . . . J 4 68.88 -25.233 5.004 1 34.02 ? C2' UPG 405 A 1 HETATM 28 C C3' UPG . . . J 4 69.452 -23.801 4.844 1 34.87 ? C3' UPG 405 A 1 HETATM 29 C C4' UPG . . . J 4 68.48 -22.793 5.468 1 34.54 ? C4' UPG 405 A 1 HETATM 30 C C5' UPG . . . J 4 68.08 -23.283 6.849 1 33.26 ? C5' UPG 405 A 1 HETATM 31 C C6' UPG . . . J 4 67.072 -22.419 7.542 1 32.63 ? C6' UPG 405 A 1 HETATM 32 O O2' UPG . . . J 4 69.64 -26.278 4.396 1 36.31 ? O2' UPG 405 A 1 HETATM 33 O O3' UPG . . . J 4 69.615 -23.527 3.44 1 33.22 ? O3' UPG 405 A 1 HETATM 34 O O4' UPG . . . J 4 69.06 -21.49 5.634 1 33.51 ? O4' UPG 405 A 1 HETATM 35 O O5' UPG . . . J 4 67.581 -24.616 6.824 1 35.9 ? O5' UPG 405 A 1 HETATM 36 O O6' UPG . . . J 4 65.956 -22.178 6.712 1 35.73 ? O6' UPG 405 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #