data_3UKK
#
_model_server_result.job_id            GezDDntpyiZUTkqFXO_BpQ 
_model_server_result.datetime_utc      '2024-11-15 03:35:09' 
_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          3ukk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":602}' 
#
_entry.id    3UKK 
#
_exptl.entry_id    3UKK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.26 
_cell.angle_gamma         90 
_cell.entry_id            3UKK 
_cell.length_a            70.66 
_cell.length_b            123.66 
_cell.length_c            156.37 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3UKK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,P 
_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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N 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 542 n n 
N1 C6 UDP sing 543 n n 
N1 C1' UDP sing 544 n n 
C2 N3 UDP sing 545 n n 
C2 O2 UDP doub 546 n n 
N3 C4 UDP sing 547 n n 
N3 HN3 UDP sing 548 n n 
C4 C5 UDP sing 549 n n 
C4 O4 UDP doub 550 n n 
C5 C6 UDP doub 551 n n 
C5 H5 UDP sing 552 n n 
C6 H6 UDP sing 553 n n 
C1' C2' UDP sing 554 n n 
C1' O4' UDP sing 555 n n 
C1' H1' UDP sing 556 n n 
C2' O2' UDP sing 557 n n 
C2' C3' UDP sing 558 n n 
C2' H2' UDP sing 559 n n 
O2' HO2' UDP sing 560 n n 
C3' C4' UDP sing 561 n n 
C3' O3' UDP sing 562 n n 
C3' H3' UDP sing 563 n n 
C4' O4' UDP sing 564 n n 
C4' C5' UDP sing 565 n n 
C4' H4' UDP sing 566 n n 
O3' HO3' UDP sing 567 n n 
C5' O5' UDP sing 568 n n 
C5' "H5'1" UDP sing 569 n n 
C5' "H5'2" UDP sing 570 n n 
O5' PA UDP sing 571 n n 
PA O1A UDP doub 572 n n 
PA O2A UDP sing 573 n n 
PA O3A UDP sing 574 n n 
O2A HOA2 UDP sing 575 n n 
O3A PB UDP sing 576 n n 
PB O1B UDP doub 577 n n 
PB O2B UDP sing 578 n n 
PB O3B UDP sing 579 n n 
O2B HOB2 UDP sing 580 n n 
O3B HOB3 UDP sing 581 n n 
#
_atom_sites.entry_id                     3UKK 
_atom_sites.fract_transf_matrix[1][1]    0.014152 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003335 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008087 
_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]    0.00657 
_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
E 2 FDA A 1 601 600 FDA FDA . 
F 3 UDP A 1 602 800 UDP UDP . 
G 2 FDA B 1 601 600 FDA FDA . 
H 3 UDP B 1 602 800 UDP UDP . 
I 4 FAD C 1 601 602 FAD FAD . 
J 3 UDP C 1 602 800 UDP UDP . 
K 2 FDA D 1 601 600 FDA FDA . 
L 3 UDP D 1 602 800 UDP UDP . 
M 5 HOH A 1 701 519 HOH HOH . 
M 5 HOH A 2 702 520 HOH HOH . 
M 5 HOH A 3 703 521 HOH HOH . 
M 5 HOH A 4 704 522 HOH HOH . 
M 5 HOH A 5 705 523 HOH HOH . 
M 5 HOH A 6 706 524 HOH HOH . 
M 5 HOH A 7 707 525 HOH HOH . 
M 5 HOH A 8 708 526 HOH HOH . 
M 5 HOH A 9 709 527 HOH HOH . 
M 5 HOH A 10 710 528 HOH HOH . 
M 5 HOH A 11 711 529 HOH HOH . 
M 5 HOH A 12 712 530 HOH HOH . 
M 5 HOH A 13 713 531 HOH HOH . 
M 5 HOH A 14 714 532 HOH HOH . 
M 5 HOH A 15 715 533 HOH HOH . 
M 5 HOH A 16 716 534 HOH HOH . 
M 5 HOH A 17 717 535 HOH HOH . 
M 5 HOH A 18 718 536 HOH HOH . 
M 5 HOH A 19 719 537 HOH HOH . 
M 5 HOH A 20 720 538 HOH HOH . 
M 5 HOH A 21 721 539 HOH HOH . 
M 5 HOH A 22 722 540 HOH HOH . 
M 5 HOH A 23 723 541 HOH HOH . 
M 5 HOH A 24 724 542 HOH HOH . 
M 5 HOH A 25 725 543 HOH HOH . 
M 5 HOH A 26 726 544 HOH HOH . 
M 5 HOH A 27 727 545 HOH HOH . 
M 5 HOH A 28 728 546 HOH HOH . 
M 5 HOH A 29 729 547 HOH HOH . 
M 5 HOH A 30 730 548 HOH HOH . 
M 5 HOH A 31 731 549 HOH HOH . 
M 5 HOH A 32 732 550 HOH HOH . 
M 5 HOH A 33 733 551 HOH HOH . 
M 5 HOH A 34 734 552 HOH HOH . 
M 5 HOH A 35 735 553 HOH HOH . 
M 5 HOH A 36 736 554 HOH HOH . 
M 5 HOH A 37 737 555 HOH HOH . 
M 5 HOH A 38 738 556 HOH HOH . 
M 5 HOH A 39 739 557 HOH HOH . 
M 5 HOH A 40 740 558 HOH HOH . 
M 5 HOH A 41 741 559 HOH HOH . 
M 5 HOH A 42 742 560 HOH HOH . 
M 5 HOH A 43 743 561 HOH HOH . 
M 5 HOH A 44 744 562 HOH HOH . 
M 5 HOH A 45 745 563 HOH HOH . 
M 5 HOH A 46 746 564 HOH HOH . 
M 5 HOH A 47 747 565 HOH HOH . 
M 5 HOH A 48 748 566 HOH HOH . 
M 5 HOH A 49 749 567 HOH HOH . 
M 5 HOH A 50 750 568 HOH HOH . 
M 5 HOH A 51 751 569 HOH HOH . 
M 5 HOH A 52 752 570 HOH HOH . 
M 5 HOH A 53 753 571 HOH HOH . 
M 5 HOH A 54 754 572 HOH HOH . 
N 5 HOH B 1 701 519 HOH HOH . 
N 5 HOH B 2 702 520 HOH HOH . 
N 5 HOH B 3 703 521 HOH HOH . 
N 5 HOH B 4 704 522 HOH HOH . 
N 5 HOH B 5 705 523 HOH HOH . 
N 5 HOH B 6 706 524 HOH HOH . 
N 5 HOH B 7 707 525 HOH HOH . 
N 5 HOH B 8 708 526 HOH HOH . 
N 5 HOH B 9 709 527 HOH HOH . 
N 5 HOH B 10 710 528 HOH HOH . 
N 5 HOH B 11 711 529 HOH HOH . 
N 5 HOH B 12 712 530 HOH HOH . 
N 5 HOH B 13 713 531 HOH HOH . 
N 5 HOH B 14 714 532 HOH HOH . 
N 5 HOH B 15 715 533 HOH HOH . 
N 5 HOH B 16 716 534 HOH HOH . 
N 5 HOH B 17 717 535 HOH HOH . 
N 5 HOH B 18 718 536 HOH HOH . 
N 5 HOH B 19 719 537 HOH HOH . 
N 5 HOH B 20 720 538 HOH HOH . 
N 5 HOH B 21 721 539 HOH HOH . 
N 5 HOH B 22 722 540 HOH HOH . 
N 5 HOH B 23 723 541 HOH HOH . 
N 5 HOH B 24 724 542 HOH HOH . 
N 5 HOH B 25 725 543 HOH HOH . 
N 5 HOH B 26 726 544 HOH HOH . 
N 5 HOH B 27 727 545 HOH HOH . 
N 5 HOH B 28 728 546 HOH HOH . 
N 5 HOH B 29 729 547 HOH HOH . 
N 5 HOH B 30 730 548 HOH HOH . 
N 5 HOH B 31 731 549 HOH HOH . 
N 5 HOH B 32 732 550 HOH HOH . 
N 5 HOH B 33 733 551 HOH HOH . 
N 5 HOH B 34 734 552 HOH HOH . 
N 5 HOH B 35 735 553 HOH HOH . 
N 5 HOH B 36 736 554 HOH HOH . 
N 5 HOH B 37 737 555 HOH HOH . 
N 5 HOH B 38 738 556 HOH HOH . 
N 5 HOH B 39 739 557 HOH HOH . 
N 5 HOH B 40 740 558 HOH HOH . 
N 5 HOH B 41 741 559 HOH HOH . 
N 5 HOH B 42 742 560 HOH HOH . 
N 5 HOH B 43 743 561 HOH HOH . 
N 5 HOH B 44 744 562 HOH HOH . 
N 5 HOH B 45 745 563 HOH HOH . 
N 5 HOH B 46 746 564 HOH HOH . 
N 5 HOH B 47 747 565 HOH HOH . 
N 5 HOH B 48 748 566 HOH HOH . 
N 5 HOH B 49 749 567 HOH HOH . 
N 5 HOH B 50 750 568 HOH HOH . 
N 5 HOH B 51 751 569 HOH HOH . 
N 5 HOH B 52 752 570 HOH HOH . 
N 5 HOH B 53 753 571 HOH HOH . 
O 5 HOH C 1 701 1 HOH HOH . 
O 5 HOH C 2 702 519 HOH HOH . 
O 5 HOH C 3 703 520 HOH HOH . 
O 5 HOH C 4 704 521 HOH HOH . 
O 5 HOH C 5 705 522 HOH HOH . 
O 5 HOH C 6 706 523 HOH HOH . 
O 5 HOH C 7 707 524 HOH HOH . 
O 5 HOH C 8 708 525 HOH HOH . 
O 5 HOH C 9 709 526 HOH HOH . 
O 5 HOH C 10 710 527 HOH HOH . 
O 5 HOH C 11 711 528 HOH HOH . 
O 5 HOH C 12 712 529 HOH HOH . 
O 5 HOH C 13 713 530 HOH HOH . 
O 5 HOH C 14 714 531 HOH HOH . 
O 5 HOH C 15 715 532 HOH HOH . 
O 5 HOH C 16 716 533 HOH HOH . 
O 5 HOH C 17 717 534 HOH HOH . 
O 5 HOH C 18 718 535 HOH HOH . 
O 5 HOH C 19 719 536 HOH HOH . 
O 5 HOH C 20 720 537 HOH HOH . 
O 5 HOH C 21 721 538 HOH HOH . 
O 5 HOH C 22 722 539 HOH HOH . 
O 5 HOH C 23 723 540 HOH HOH . 
O 5 HOH C 24 724 541 HOH HOH . 
O 5 HOH C 25 725 542 HOH HOH . 
O 5 HOH C 26 726 543 HOH HOH . 
O 5 HOH C 27 727 544 HOH HOH . 
O 5 HOH C 28 728 545 HOH HOH . 
O 5 HOH C 29 729 546 HOH HOH . 
O 5 HOH C 30 730 547 HOH HOH . 
O 5 HOH C 31 731 548 HOH HOH . 
O 5 HOH C 32 732 549 HOH HOH . 
O 5 HOH C 33 733 550 HOH HOH . 
O 5 HOH C 34 734 551 HOH HOH . 
O 5 HOH C 35 735 552 HOH HOH . 
O 5 HOH C 36 736 553 HOH HOH . 
O 5 HOH C 37 737 555 HOH HOH . 
P 5 HOH D 1 701 519 HOH HOH . 
P 5 HOH D 2 702 520 HOH HOH . 
P 5 HOH D 3 703 521 HOH HOH . 
P 5 HOH D 4 704 522 HOH HOH . 
P 5 HOH D 5 705 523 HOH HOH . 
P 5 HOH D 6 706 524 HOH HOH . 
P 5 HOH D 7 707 525 HOH HOH . 
P 5 HOH D 8 708 526 HOH HOH . 
P 5 HOH D 9 709 527 HOH HOH . 
P 5 HOH D 10 710 528 HOH HOH . 
P 5 HOH D 11 711 529 HOH HOH . 
P 5 HOH D 12 712 530 HOH HOH . 
P 5 HOH D 13 713 531 HOH HOH . 
P 5 HOH D 14 714 532 HOH HOH . 
P 5 HOH D 15 715 533 HOH HOH . 
P 5 HOH D 16 716 534 HOH HOH . 
P 5 HOH D 17 717 535 HOH HOH . 
P 5 HOH D 18 718 536 HOH HOH . 
P 5 HOH D 19 719 537 HOH HOH . 
P 5 HOH D 20 720 538 HOH HOH . 
P 5 HOH D 21 721 539 HOH HOH . 
P 5 HOH D 22 722 540 HOH HOH . 
P 5 HOH D 23 723 541 HOH HOH . 
P 5 HOH D 24 724 542 HOH HOH . 
P 5 HOH D 25 725 543 HOH HOH . 
P 5 HOH D 26 726 544 HOH HOH . 
P 5 HOH D 27 727 545 HOH HOH . 
P 5 HOH D 28 728 546 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 . . . L 3 32.546 -19.223 12.734 1 95.02 ? N1 UDP 602 D 1 
HETATM 2 C C2 UDP . . . L 3 31.757 -20.321 13.028 1 96.01 ? C2 UDP 602 D 1 
HETATM 3 N N3 UDP . . . L 3 31.094 -20.984 12.016 1 108.7 ? N3 UDP 602 D 1 
HETATM 4 C C4 UDP . . . L 3 31.107 -20.48 10.728 1 95.5 ? C4 UDP 602 D 1 
HETATM 5 C C5 UDP . . . L 3 31.855 -19.333 10.458 1 76.99 ? C5 UDP 602 D 1 
HETATM 6 C C6 UDP . . . L 3 32.396 -18.61 11.519 1 93.32 ? C6 UDP 602 D 1 
HETATM 7 O O2 UDP . . . L 3 31.619 -20.688 14.195 1 55.85 ? O2 UDP 602 D 1 
HETATM 8 O O4 UDP . . . L 3 30.459 -21.042 9.833 1 73.69 ? O4 UDP 602 D 1 
HETATM 9 C C1' UDP . . . L 3 33.231 -18.541 13.847 1 90.11 ? C1' UDP 602 D 1 
HETATM 10 C C2' UDP . . . L 3 34.706 -18.327 13.538 1 85.59 ? C2' UDP 602 D 1 
HETATM 11 O O2' UDP . . . L 3 35.475 -18.823 14.609 1 92.47 ? O2' UDP 602 D 1 
HETATM 12 C C3' UDP . . . L 3 34.885 -16.828 13.5 1 109.95 ? C3' UDP 602 D 1 
HETATM 13 C C4' UDP . . . L 3 33.675 -16.309 14.257 1 100.54 ? C4' UDP 602 D 1 
HETATM 14 O O4' UDP . . . L 3 32.659 -17.268 14.066 1 84 ? O4' UDP 602 D 1 
HETATM 15 O O3' UDP . . . L 3 36.086 -16.473 14.145 1 77.05 ? O3' UDP 602 D 1 
HETATM 16 C C5' UDP . . . L 3 33.199 -14.944 13.778 1 106.58 ? C5' UDP 602 D 1 
HETATM 17 O O5' UDP . . . L 3 32.746 -15.014 12.446 1 117.01 ? O5' UDP 602 D 1 
HETATM 18 P PA UDP . . . L 3 32.391 -13.635 11.699 1 113.97 ? PA UDP 602 D 1 
HETATM 19 O O1A UDP . . . L 3 31.239 -12.988 12.359 1 122.88 ? O1A UDP 602 D 1 
HETATM 20 O O2A UDP . . . L 3 32.14 -13.844 10.254 1 79.05 ? O2A UDP 602 D 1 
HETATM 21 O O3A UDP . . . L 3 33.707 -12.763 11.998 1 100.36 ? O3A UDP 602 D 1 
HETATM 22 P PB UDP . . . L 3 34.106 -11.502 11.093 1 113.84 ? PB UDP 602 D 1 
HETATM 23 O O1B UDP . . . L 3 35.345 -11.808 10.339 1 81.7 ? O1B UDP 602 D 1 
HETATM 24 O O2B UDP . . . L 3 34.29 -10.337 11.988 1 112.45 ? O2B UDP 602 D 1 
HETATM 25 O O3B UDP . . . L 3 33.017 -11.208 10.134 1 134.41 ? O3B UDP 602 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    50 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#