data_6KVK
#
_model_server_result.job_id            41AcMu8WCsGDHcVsdnUZgA 
_model_server_result.datetime_utc      '2025-07-16 02:07:47' 
_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          6kvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    6KVK 
#
_exptl.entry_id    6KVK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "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         120 
_cell.entry_id            6KVK 
_cell.length_a            98.013 
_cell.length_b            98.013 
_cell.length_c            89.529 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KVK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
N1 C2 UDP sing 436 n n 
N1 C6 UDP sing 437 n n 
N1 C1' UDP sing 438 n n 
C2 N3 UDP sing 439 n n 
C2 O2 UDP doub 440 n n 
N3 C4 UDP sing 441 n n 
N3 HN3 UDP sing 442 n n 
C4 C5 UDP sing 443 n n 
C4 O4 UDP doub 444 n n 
C5 C6 UDP doub 445 n n 
C5 H5 UDP sing 446 n n 
C6 H6 UDP sing 447 n n 
C1' C2' UDP sing 448 n n 
C1' O4' UDP sing 449 n n 
C1' H1' UDP sing 450 n n 
C2' O2' UDP sing 451 n n 
C2' C3' UDP sing 452 n n 
C2' H2' UDP sing 453 n n 
O2' HO2' UDP sing 454 n n 
C3' C4' UDP sing 455 n n 
C3' O3' UDP sing 456 n n 
C3' H3' UDP sing 457 n n 
C4' O4' UDP sing 458 n n 
C4' C5' UDP sing 459 n n 
C4' H4' UDP sing 460 n n 
O3' HO3' UDP sing 461 n n 
C5' O5' UDP sing 462 n n 
C5' "H5'1" UDP sing 463 n n 
C5' "H5'2" UDP sing 464 n n 
O5' PA UDP sing 465 n n 
PA O1A UDP doub 466 n n 
PA O2A UDP sing 467 n n 
PA O3A UDP sing 468 n n 
O2A HOA2 UDP sing 469 n n 
O3A PB UDP sing 470 n n 
PB O1B UDP doub 471 n n 
PB O2B UDP sing 472 n n 
PB O3B UDP sing 473 n n 
O2B HOB2 UDP sing 474 n n 
O3B HOB3 UDP sing 475 n n 
#
_atom_sites.entry_id                     6KVK 
_atom_sites.fract_transf_matrix[1][1]    0.010203 
_atom_sites.fract_transf_matrix[1][2]    0.005891 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011781 
_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]    0.01117 
_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
B 2 UDP A 1 501 1 UDP UDP . 
C 3 DX0 A 1 502 1 DX0 DRG . 
D 4 HOH A 1 601 55 HOH HOH . 
D 4 HOH A 2 602 94 HOH HOH . 
D 4 HOH A 3 603 2 HOH HOH . 
D 4 HOH A 4 604 75 HOH HOH . 
D 4 HOH A 5 605 69 HOH HOH . 
D 4 HOH A 6 606 90 HOH HOH . 
D 4 HOH A 7 607 12 HOH HOH . 
D 4 HOH A 8 608 7 HOH HOH . 
D 4 HOH A 9 609 41 HOH HOH . 
D 4 HOH A 10 610 78 HOH HOH . 
D 4 HOH A 11 611 21 HOH HOH . 
D 4 HOH A 12 612 86 HOH HOH . 
D 4 HOH A 13 613 1 HOH HOH . 
D 4 HOH A 14 614 16 HOH HOH . 
D 4 HOH A 15 615 76 HOH HOH . 
D 4 HOH A 16 616 57 HOH HOH . 
D 4 HOH A 17 617 23 HOH HOH . 
D 4 HOH A 18 618 13 HOH HOH . 
D 4 HOH A 19 619 67 HOH HOH . 
D 4 HOH A 20 620 8 HOH HOH . 
D 4 HOH A 21 621 44 HOH HOH . 
D 4 HOH A 22 622 11 HOH HOH . 
D 4 HOH A 23 623 65 HOH HOH . 
D 4 HOH A 24 624 19 HOH HOH . 
D 4 HOH A 25 625 79 HOH HOH . 
D 4 HOH A 26 626 33 HOH HOH . 
D 4 HOH A 27 627 48 HOH HOH . 
D 4 HOH A 28 628 9 HOH HOH . 
D 4 HOH A 29 629 38 HOH HOH . 
D 4 HOH A 30 630 53 HOH HOH . 
D 4 HOH A 31 631 47 HOH HOH . 
D 4 HOH A 32 632 5 HOH HOH . 
D 4 HOH A 33 633 80 HOH HOH . 
D 4 HOH A 34 634 34 HOH HOH . 
D 4 HOH A 35 635 37 HOH HOH . 
D 4 HOH A 36 636 26 HOH HOH . 
D 4 HOH A 37 637 32 HOH HOH . 
D 4 HOH A 38 638 82 HOH HOH . 
D 4 HOH A 39 639 29 HOH HOH . 
D 4 HOH A 40 640 56 HOH HOH . 
D 4 HOH A 41 641 3 HOH HOH . 
D 4 HOH A 42 642 30 HOH HOH . 
D 4 HOH A 43 643 22 HOH HOH . 
D 4 HOH A 44 644 4 HOH HOH . 
D 4 HOH A 45 645 20 HOH HOH . 
D 4 HOH A 46 646 28 HOH HOH . 
D 4 HOH A 47 647 31 HOH HOH . 
D 4 HOH A 48 648 49 HOH HOH . 
D 4 HOH A 49 649 52 HOH HOH . 
D 4 HOH A 50 650 6 HOH HOH . 
D 4 HOH A 51 651 50 HOH HOH . 
D 4 HOH A 52 652 83 HOH HOH . 
D 4 HOH A 53 653 39 HOH HOH . 
D 4 HOH A 54 654 93 HOH HOH . 
D 4 HOH A 55 655 74 HOH HOH . 
D 4 HOH A 56 656 24 HOH HOH . 
D 4 HOH A 57 657 27 HOH HOH . 
D 4 HOH A 58 658 62 HOH HOH . 
D 4 HOH A 59 659 40 HOH HOH . 
D 4 HOH A 60 660 87 HOH HOH . 
D 4 HOH A 61 661 58 HOH HOH . 
D 4 HOH A 62 662 61 HOH HOH . 
D 4 HOH A 63 663 68 HOH HOH . 
D 4 HOH A 64 664 51 HOH HOH . 
D 4 HOH A 65 665 92 HOH HOH . 
D 4 HOH A 66 666 25 HOH HOH . 
D 4 HOH A 67 667 17 HOH HOH . 
D 4 HOH A 68 668 66 HOH HOH . 
D 4 HOH A 69 669 73 HOH HOH . 
D 4 HOH A 70 670 81 HOH HOH . 
D 4 HOH A 71 671 15 HOH HOH . 
D 4 HOH A 72 672 35 HOH HOH . 
D 4 HOH A 73 673 72 HOH HOH . 
D 4 HOH A 74 674 63 HOH HOH . 
D 4 HOH A 75 675 64 HOH HOH . 
D 4 HOH A 76 676 84 HOH HOH . 
D 4 HOH A 77 677 91 HOH HOH . 
D 4 HOH A 78 678 85 HOH HOH . 
D 4 HOH A 79 679 18 HOH HOH . 
D 4 HOH A 80 680 70 HOH HOH . 
D 4 HOH A 81 681 95 HOH HOH . 
D 4 HOH A 82 682 60 HOH HOH . 
D 4 HOH A 83 683 77 HOH HOH . 
D 4 HOH A 84 684 46 HOH HOH . 
D 4 HOH A 85 685 59 HOH HOH . 
D 4 HOH A 86 686 54 HOH HOH . 
D 4 HOH A 87 687 10 HOH HOH . 
D 4 HOH A 88 688 71 HOH HOH . 
D 4 HOH A 89 689 88 HOH HOH . 
D 4 HOH A 90 690 45 HOH HOH . 
D 4 HOH A 91 691 36 HOH HOH . 
D 4 HOH A 92 692 43 HOH HOH . 
D 4 HOH A 93 693 96 HOH HOH . 
D 4 HOH A 94 694 89 HOH HOH . 
D 4 HOH A 95 695 42 HOH HOH . 
D 4 HOH A 96 696 14 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 UDP . . . B 2 -16.321 14.627 2.463 1 48.11 ? N1 UDP 501 A 1 
HETATM 2 C C2 UDP . . . B 2 -15.609 14.202 3.556 1 48.42 ? C2 UDP 501 A 1 
HETATM 3 N N3 UDP . . . B 2 -14.285 13.851 3.415 1 47.82 ? N3 UDP 501 A 1 
HETATM 4 C C4 UDP . . . B 2 -13.668 13.91 2.183 1 49.29 ? C4 UDP 501 A 1 
HETATM 5 C C5 UDP . . . B 2 -14.398 14.341 1.077 1 49.81 ? C5 UDP 501 A 1 
HETATM 6 C C6 UDP . . . B 2 -15.702 14.805 1.255 1 47.65 ? C6 UDP 501 A 1 
HETATM 7 O O2 UDP . . . B 2 -16.142 14.169 4.665 1 51.05 ? O2 UDP 501 A 1 
HETATM 8 O O4 UDP . . . B 2 -12.479 13.588 2.076 1 48.8 ? O4 UDP 501 A 1 
HETATM 9 C C1' UDP . . . B 2 -17.728 14.992 2.644 1 46.74 ? C1' UDP 501 A 1 
HETATM 10 C C2' UDP . . . B 2 -17.891 16.491 2.586 1 47.49 ? C2' UDP 501 A 1 
HETATM 11 O O2' UDP . . . B 2 -17.659 17.114 3.832 1 45.16 ? O2' UDP 501 A 1 
HETATM 12 C C3' UDP . . . B 2 -19.321 16.587 2.092 1 47.38 ? C3' UDP 501 A 1 
HETATM 13 C C4' UDP . . . B 2 -19.575 15.31 1.277 1 51.04 ? C4' UDP 501 A 1 
HETATM 14 O O4' UDP . . . B 2 -18.509 14.445 1.597 1 50.55 ? O4' UDP 501 A 1 
HETATM 15 O O3' UDP . . . B 2 -20.184 16.636 3.202 1 45.11 ? O3' UDP 501 A 1 
HETATM 16 C C5' UDP . . . B 2 -19.551 15.517 -0.215 1 49.2 ? C5' UDP 501 A 1 
HETATM 17 O O5' UDP . . . B 2 -20.734 16.174 -0.596 1 56.24 ? O5' UDP 501 A 1 
HETATM 18 P PA UDP . . . B 2 -20.745 17.249 -1.782 1 58.12 ? PA UDP 501 A 1 
HETATM 19 O O1A UDP . . . B 2 -22.121 17.638 -1.945 1 55.88 ? O1A UDP 501 A 1 
HETATM 20 O O2A UDP . . . B 2 -19.938 18.446 -1.482 1 62.1 -1 O2A UDP 501 A 1 
HETATM 21 O O3A UDP . . . B 2 -20.148 16.538 -3.06 1 73.48 ? O3A UDP 501 A 1 
HETATM 22 P PB UDP . . . B 2 -20.639 15.175 -3.758 1 72.76 ? PB UDP 501 A 1 
HETATM 23 O O1B UDP . . . B 2 -20.859 15.446 -5.196 1 72.97 -1 O1B UDP 501 A 1 
HETATM 24 O O2B UDP . . . B 2 -21.881 14.591 -3.205 1 66.9 ? O2B UDP 501 A 1 
HETATM 25 O O3B UDP . . . B 2 -19.495 14.268 -3.53 1 60.71 -1 O3B UDP 501 A 1 
HETATM 26 H HN3 UDP . . . B 2 -13.745 13.537 4.246 1 57.38 ? HN3 UDP 501 A 1 
HETATM 27 H H5 UDP . . . B 2 -13.909 14.45 0.109 1 59.77 ? H5 UDP 501 A 1 
HETATM 28 H H6 UDP . . . B 2 -16.269 15.179 0.402 1 57.18 ? H6 UDP 501 A 1 
HETATM 29 H H1' UDP . . . B 2 -18.089 14.633 3.608 1 56.09 ? H1' UDP 501 A 1 
HETATM 30 H H2' UDP . . . B 2 -17.221 16.895 1.827 1 56.99 ? H2' UDP 501 A 1 
HETATM 31 H HO2' UDP . . . B 2 -18.494 17.508 4.16 1 54.19 ? HO2' UDP 501 A 1 
HETATM 32 H H3' UDP . . . B 2 -19.44 17.467 1.459 1 56.85 ? H3' UDP 501 A 1 
HETATM 33 H H4' UDP . . . B 2 -20.528 14.872 1.571 1 61.25 ? H4' UDP 501 A 1 
HETATM 34 H HO3' UDP . . . B 2 -20.756 15.84 3.205 1 54.13 ? HO3' UDP 501 A 1 
HETATM 35 H "H5'1" UDP . . . B 2 -18.686 16.117 -0.494 1 59.04 ? "H5'1" UDP 501 A 1 
HETATM 36 H "H5'2" UDP . . . B 2 -19.481 14.554 -0.722 1 59.04 ? "H5'2" UDP 501 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#