data_3INT # _model_server_result.job_id Tl4hh705Yr2wJrpE_UmcRg _model_server_result.datetime_utc '2024-11-15 02:21:57' _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 3int # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":392}' # _entry.id 3INT # _exptl.entry_id 3INT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 3INT _cell.length_a 94.078 _cell.length_b 94.078 _cell.length_c 129.443 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3INT _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,C,D,G 2 1 B,E,F,H 3 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id GDU _chem_comp.mon_nstd_flag . _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE # 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 GDU sing 176 n n N1 C6 GDU sing 177 n n N1 C1D GDU sing 178 n n C2 N3 GDU sing 179 n n C2 O2 GDU doub 180 n n N3 C4 GDU sing 181 n n N3 HN3 GDU sing 182 n n C4 C5 GDU sing 183 n n C4 O4 GDU doub 184 n n C5 C6 GDU doub 185 n n C5 H5 GDU sing 186 n n C6 H6 GDU sing 187 n n C1D C2D GDU sing 188 n n C1D O4D GDU sing 189 n n C1D H1D GDU sing 190 n n C2D O2D GDU sing 191 n n C2D C3D GDU sing 192 n n C2D H2D GDU sing 193 n n O2D HO2' GDU sing 194 n n C3D C4D GDU sing 195 n n C3D O3D GDU sing 196 n n C3D H3D GDU sing 197 n n C4D O4D GDU sing 198 n n C4D C5D GDU sing 199 n n C4D H4D GDU sing 200 n n O3D HO3' GDU sing 201 n n C5D O5D GDU sing 202 n n C5D "H5'1" GDU sing 203 n n C5D "H5'2" GDU sing 204 n n O5D PA GDU sing 205 n n PA O1A GDU doub 206 n n PA O2A GDU sing 207 n n PA O3A GDU sing 208 n n O2A HOA2 GDU sing 209 n n O3A PB GDU sing 210 n n PB O1B GDU doub 211 n n PB O2B GDU sing 212 n n PB O3B GDU sing 213 n n O2B HOB2 GDU sing 214 n n O3B C1' GDU sing 215 n n C1' C2' GDU sing 216 n n C1' O5' GDU sing 217 n n C1' H1' GDU sing 218 n n C2' C3' GDU sing 219 n n C2' O2' GDU sing 220 n n C2' H2' GDU sing 221 n n C3' C4' GDU sing 222 n n C3' O3' GDU sing 223 n n C3' H3' GDU sing 224 n n C4' C5' GDU sing 225 n n C4' O4' GDU sing 226 n n C4' H4' GDU sing 227 n n C5' C6' GDU sing 228 n n C5' O5' GDU sing 229 n n C5' H5' GDU sing 230 n n C6' O6' GDU sing 231 n n C6' "H6'1" GDU sing 232 n n C6' "H6'2" GDU sing 233 n n O2' HO2A GDU sing 234 n n O3' HO3A GDU sing 235 n n O4' HO4' GDU sing 236 n n O6' HO6' GDU sing 237 n n # _atom_sites.entry_id 3INT _atom_sites.fract_transf_matrix[1][1] 0.010629 _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] 0.010629 _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] 0.007725 _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 FDA A 1 391 385 FDA FDA . D 3 UDP A 1 392 387 UDP UDP . E 2 FDA B 1 391 386 FDA FDA . F 4 GDU B 1 392 388 GDU GDU . G 5 HOH A 1 393 389 HOH HOH . G 5 HOH A 2 394 394 HOH HOH . G 5 HOH A 3 395 395 HOH HOH . G 5 HOH A 4 396 396 HOH HOH . G 5 HOH A 5 397 390 HOH HOH . G 5 HOH A 6 398 398 HOH HOH . G 5 HOH A 7 399 392 HOH HOH . G 5 HOH A 8 400 400 HOH HOH . G 5 HOH A 9 401 401 HOH HOH . G 5 HOH A 10 402 402 HOH HOH . G 5 HOH A 11 403 403 HOH HOH . G 5 HOH A 12 404 404 HOH HOH . G 5 HOH A 13 408 408 HOH HOH . G 5 HOH A 14 409 409 HOH HOH . G 5 HOH A 15 410 410 HOH HOH . G 5 HOH A 16 413 413 HOH HOH . G 5 HOH A 17 414 414 HOH HOH . G 5 HOH A 18 418 418 HOH HOH . G 5 HOH A 19 420 420 HOH HOH . G 5 HOH A 20 421 421 HOH HOH . G 5 HOH A 21 422 422 HOH HOH . G 5 HOH A 22 426 426 HOH HOH . G 5 HOH A 23 429 429 HOH HOH . G 5 HOH A 24 431 431 HOH HOH . G 5 HOH A 25 432 432 HOH HOH . G 5 HOH A 26 434 434 HOH HOH . G 5 HOH A 27 435 435 HOH HOH . G 5 HOH A 28 438 438 HOH HOH . G 5 HOH A 29 439 439 HOH HOH . G 5 HOH A 30 440 440 HOH HOH . G 5 HOH A 31 441 441 HOH HOH . G 5 HOH A 32 442 442 HOH HOH . G 5 HOH A 33 443 443 HOH HOH . G 5 HOH A 34 444 444 HOH HOH . G 5 HOH A 35 445 445 HOH HOH . G 5 HOH A 36 452 452 HOH HOH . G 5 HOH A 37 453 453 HOH HOH . G 5 HOH A 38 455 455 HOH HOH . G 5 HOH A 39 456 456 HOH HOH . G 5 HOH A 40 459 459 HOH HOH . G 5 HOH A 41 461 461 HOH HOH . G 5 HOH A 42 462 462 HOH HOH . G 5 HOH A 43 465 465 HOH HOH . G 5 HOH A 44 467 467 HOH HOH . G 5 HOH A 45 470 470 HOH HOH . G 5 HOH A 46 471 471 HOH HOH . G 5 HOH A 47 472 472 HOH HOH . G 5 HOH A 48 473 473 HOH HOH . G 5 HOH A 49 474 474 HOH HOH . G 5 HOH A 50 475 475 HOH HOH . G 5 HOH A 51 477 477 HOH HOH . G 5 HOH A 52 481 481 HOH HOH . G 5 HOH A 53 483 483 HOH HOH . G 5 HOH A 54 484 484 HOH HOH . G 5 HOH A 55 488 488 HOH HOH . G 5 HOH A 56 489 489 HOH HOH . G 5 HOH A 57 492 492 HOH HOH . G 5 HOH A 58 493 493 HOH HOH . G 5 HOH A 59 494 494 HOH HOH . G 5 HOH A 60 496 496 HOH HOH . G 5 HOH A 61 498 498 HOH HOH . G 5 HOH A 62 499 499 HOH HOH . G 5 HOH A 63 501 501 HOH HOH . G 5 HOH A 64 502 502 HOH HOH . G 5 HOH A 65 505 505 HOH HOH . G 5 HOH A 66 508 508 HOH HOH . G 5 HOH A 67 510 510 HOH HOH . G 5 HOH A 68 513 513 HOH HOH . G 5 HOH A 69 515 515 HOH HOH . G 5 HOH A 70 517 517 HOH HOH . G 5 HOH A 71 518 518 HOH HOH . G 5 HOH A 72 519 519 HOH HOH . G 5 HOH A 73 520 520 HOH HOH . G 5 HOH A 74 521 521 HOH HOH . G 5 HOH A 75 524 524 HOH HOH . G 5 HOH A 76 525 525 HOH HOH . G 5 HOH A 77 527 527 HOH HOH . G 5 HOH A 78 531 531 HOH HOH . G 5 HOH A 79 533 533 HOH HOH . G 5 HOH A 80 535 535 HOH HOH . G 5 HOH A 81 538 538 HOH HOH . G 5 HOH A 82 539 539 HOH HOH . G 5 HOH A 83 546 546 HOH HOH . G 5 HOH A 84 549 549 HOH HOH . G 5 HOH A 85 550 550 HOH HOH . G 5 HOH A 86 551 551 HOH HOH . G 5 HOH A 87 552 552 HOH HOH . G 5 HOH A 88 553 553 HOH HOH . G 5 HOH A 89 554 554 HOH HOH . G 5 HOH A 90 555 555 HOH HOH . G 5 HOH A 91 557 557 HOH HOH . G 5 HOH A 92 558 558 HOH HOH . G 5 HOH A 93 560 560 HOH HOH . G 5 HOH A 94 561 561 HOH HOH . G 5 HOH A 95 562 562 HOH HOH . G 5 HOH A 96 563 563 HOH HOH . G 5 HOH A 97 568 568 HOH HOH . G 5 HOH A 98 578 578 HOH HOH . G 5 HOH A 99 579 579 HOH HOH . G 5 HOH A 100 580 580 HOH HOH . G 5 HOH A 101 581 581 HOH HOH . G 5 HOH A 102 582 582 HOH HOH . G 5 HOH A 103 583 583 HOH HOH . G 5 HOH A 104 584 584 HOH HOH . H 5 HOH B 1 393 393 HOH HOH . H 5 HOH B 2 394 391 HOH HOH . H 5 HOH B 3 397 397 HOH HOH . H 5 HOH B 4 399 399 HOH HOH . H 5 HOH B 5 405 405 HOH HOH . H 5 HOH B 6 406 406 HOH HOH . H 5 HOH B 7 407 407 HOH HOH . H 5 HOH B 8 411 411 HOH HOH . H 5 HOH B 9 412 412 HOH HOH . H 5 HOH B 10 415 415 HOH HOH . H 5 HOH B 11 416 416 HOH HOH . H 5 HOH B 12 417 417 HOH HOH . H 5 HOH B 13 419 419 HOH HOH . H 5 HOH B 14 423 423 HOH HOH . H 5 HOH B 15 424 424 HOH HOH . H 5 HOH B 16 425 425 HOH HOH . H 5 HOH B 17 427 427 HOH HOH . H 5 HOH B 18 428 428 HOH HOH . H 5 HOH B 19 430 430 HOH HOH . H 5 HOH B 20 433 433 HOH HOH . H 5 HOH B 21 436 436 HOH HOH . H 5 HOH B 22 437 437 HOH HOH . H 5 HOH B 23 446 446 HOH HOH . H 5 HOH B 24 447 447 HOH HOH . H 5 HOH B 25 448 448 HOH HOH . H 5 HOH B 26 449 449 HOH HOH . H 5 HOH B 27 450 450 HOH HOH . H 5 HOH B 28 451 451 HOH HOH . H 5 HOH B 29 454 454 HOH HOH . H 5 HOH B 30 457 457 HOH HOH . H 5 HOH B 31 458 458 HOH HOH . H 5 HOH B 32 460 460 HOH HOH . H 5 HOH B 33 463 463 HOH HOH . H 5 HOH B 34 464 464 HOH HOH . H 5 HOH B 35 466 466 HOH HOH . H 5 HOH B 36 468 468 HOH HOH . H 5 HOH B 37 469 469 HOH HOH . H 5 HOH B 38 476 476 HOH HOH . H 5 HOH B 39 478 478 HOH HOH . H 5 HOH B 40 479 479 HOH HOH . H 5 HOH B 41 480 480 HOH HOH . H 5 HOH B 42 482 482 HOH HOH . H 5 HOH B 43 485 485 HOH HOH . H 5 HOH B 44 486 486 HOH HOH . H 5 HOH B 45 487 487 HOH HOH . H 5 HOH B 46 490 490 HOH HOH . H 5 HOH B 47 491 491 HOH HOH . H 5 HOH B 48 495 495 HOH HOH . H 5 HOH B 49 497 497 HOH HOH . H 5 HOH B 50 500 500 HOH HOH . H 5 HOH B 51 503 503 HOH HOH . H 5 HOH B 52 504 504 HOH HOH . H 5 HOH B 53 506 506 HOH HOH . H 5 HOH B 54 507 507 HOH HOH . H 5 HOH B 55 509 509 HOH HOH . H 5 HOH B 56 511 511 HOH HOH . H 5 HOH B 57 512 512 HOH HOH . H 5 HOH B 58 514 514 HOH HOH . H 5 HOH B 59 516 516 HOH HOH . H 5 HOH B 60 522 522 HOH HOH . H 5 HOH B 61 523 523 HOH HOH . H 5 HOH B 62 526 526 HOH HOH . H 5 HOH B 63 528 528 HOH HOH . H 5 HOH B 64 529 529 HOH HOH . H 5 HOH B 65 530 530 HOH HOH . H 5 HOH B 66 532 532 HOH HOH . H 5 HOH B 67 534 534 HOH HOH . H 5 HOH B 68 536 536 HOH HOH . H 5 HOH B 69 537 537 HOH HOH . H 5 HOH B 70 540 540 HOH HOH . H 5 HOH B 71 541 541 HOH HOH . H 5 HOH B 72 542 542 HOH HOH . H 5 HOH B 73 543 543 HOH HOH . H 5 HOH B 74 544 544 HOH HOH . H 5 HOH B 75 545 545 HOH HOH . H 5 HOH B 76 547 547 HOH HOH . H 5 HOH B 77 548 548 HOH HOH . H 5 HOH B 78 556 556 HOH HOH . H 5 HOH B 79 559 559 HOH HOH . H 5 HOH B 80 564 564 HOH HOH . H 5 HOH B 81 565 565 HOH HOH . H 5 HOH B 82 566 566 HOH HOH . H 5 HOH B 83 567 567 HOH HOH . H 5 HOH B 84 569 569 HOH HOH . H 5 HOH B 85 570 570 HOH HOH . H 5 HOH B 86 571 571 HOH HOH . H 5 HOH B 87 572 572 HOH HOH . H 5 HOH B 88 573 573 HOH HOH . H 5 HOH B 89 574 574 HOH HOH . H 5 HOH B 90 575 575 HOH HOH . H 5 HOH B 91 576 576 HOH HOH . H 5 HOH B 92 577 577 HOH HOH . H 5 HOH B 93 585 585 HOH HOH . H 5 HOH B 94 586 586 HOH HOH . H 5 HOH B 95 587 587 HOH HOH . H 5 HOH B 96 588 588 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 GDU . . . F 4 -17.743 -54.377 4.645 1 68.45 ? N1 GDU 392 B 1 HETATM 2 C C2 GDU . . . F 4 -18.906 -53.719 5.073 1 69.39 ? C2 GDU 392 B 1 HETATM 3 N N3 GDU . . . F 4 -19.231 -52.522 4.582 1 68.41 ? N3 GDU 392 B 1 HETATM 4 C C4 GDU . . . F 4 -18.465 -51.914 3.681 1 68.11 ? C4 GDU 392 B 1 HETATM 5 C C5 GDU . . . F 4 -17.313 -52.539 3.243 1 68.36 ? C5 GDU 392 B 1 HETATM 6 C C6 GDU . . . F 4 -16.969 -53.785 3.747 1 70.12 ? C6 GDU 392 B 1 HETATM 7 O O2 GDU . . . F 4 -19.654 -54.242 5.919 1 72.86 ? O2 GDU 392 B 1 HETATM 8 O O4 GDU . . . F 4 -18.777 -50.798 3.219 1 67.6 ? O4 GDU 392 B 1 HETATM 9 C C1D GDU . . . F 4 -17.322 -55.676 5.164 1 67.82 ? C1D GDU 392 B 1 HETATM 10 C C2D GDU . . . F 4 -17.675 -56.81 4.234 1 68.32 ? C2D GDU 392 B 1 HETATM 11 O O2D GDU . . . F 4 -17.539 -58.002 5 1 64.84 ? O2D GDU 392 B 1 HETATM 12 C C3D GDU . . . F 4 -16.567 -56.734 3.209 1 67.9 ? C3D GDU 392 B 1 HETATM 13 C C4D GDU . . . F 4 -15.355 -56.353 4.053 1 68.36 ? C4D GDU 392 B 1 HETATM 14 O O4D GDU . . . F 4 -15.896 -55.678 5.19 1 67.19 ? O4D GDU 392 B 1 HETATM 15 O O3D GDU . . . F 4 -16.401 -57.976 2.527 1 65.25 ? O3D GDU 392 B 1 HETATM 16 C C5D GDU . . . F 4 -14.336 -55.479 3.332 1 67.19 ? C5D GDU 392 B 1 HETATM 17 O O5D GDU . . . F 4 -13.549 -56.299 2.484 1 67.7 ? O5D GDU 392 B 1 HETATM 18 P PA GDU . . . F 4 -12.889 -55.718 1.151 1 67.44 ? PA GDU 392 B 1 HETATM 19 O O1A GDU . . . F 4 -13.174 -54.27 0.975 1 67.17 ? O1A GDU 392 B 1 HETATM 20 O O2A GDU . . . F 4 -11.42 -55.979 1.178 1 64.12 ? O2A GDU 392 B 1 HETATM 21 O O3A GDU . . . F 4 -13.622 -56.489 -0.032 1 66.27 ? O3A GDU 392 B 1 HETATM 22 P PB GDU . . . F 4 -13.059 -56.52 -1.53 1 65.39 ? PB GDU 392 B 1 HETATM 23 O O1B GDU . . . F 4 -14.189 -56.631 -2.498 1 64.6 ? O1B GDU 392 B 1 HETATM 24 O O2B GDU . . . F 4 -12.108 -57.662 -1.675 1 64.07 ? O2B GDU 392 B 1 HETATM 25 O O3B GDU . . . F 4 -12.281 -55.144 -1.764 1 64.03 ? O3B GDU 392 B 1 HETATM 26 C C1' GDU . . . F 4 -11.261 -55.038 -2.749 1 60.47 ? C1' GDU 392 B 1 HETATM 27 C C2' GDU . . . F 4 -9.889 -55.101 -2.104 1 58.47 ? C2' GDU 392 B 1 HETATM 28 C C3' GDU . . . F 4 -9.675 -53.882 -1.23 1 59.16 ? C3' GDU 392 B 1 HETATM 29 C C4' GDU . . . F 4 -9.798 -52.667 -2.105 1 60.18 ? C4' GDU 392 B 1 HETATM 30 C C5' GDU . . . F 4 -11.168 -52.63 -2.731 1 59.49 ? C5' GDU 392 B 1 HETATM 31 C C6' GDU . . . F 4 -11.238 -51.427 -3.66 1 56.29 ? C6' GDU 392 B 1 HETATM 32 O O2' GDU . . . F 4 -9.811 -56.277 -1.31 1 57.25 ? O2' GDU 392 B 1 HETATM 33 O O3' GDU . . . F 4 -8.378 -53.872 -0.651 1 56.7 ? O3' GDU 392 B 1 HETATM 34 O O4' GDU . . . F 4 -8.762 -52.526 -3.059 1 63.46 ? O4' GDU 392 B 1 HETATM 35 O O5' GDU . . . F 4 -11.412 -53.825 -3.472 1 59.38 ? O5' GDU 392 B 1 HETATM 36 O O6' GDU . . . F 4 -11.538 -50.257 -2.908 1 55.04 ? O6' GDU 392 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #