data_3DL6
#
_model_server_result.job_id            AX-5t8mZzocuiCxvthaIQg 
_model_server_result.datetime_utc      '2024-11-14 04:47:27' 
_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          3dl6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":615}' 
#
_entry.id    3DL6 
#
_exptl.entry_id    3DL6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.94 
_cell.angle_gamma         90 
_cell.entry_id            3DL6 
_cell.length_a            214.906 
_cell.length_b            116.921 
_cell.length_c            220.948 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DL6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
C,D,N,O,P,Q,R,S,T,U,BA,CA 1 1 
A,B,F,G,H,I,J,K,L,M,Z,AA 2 1 
E,V,W,X,Y,DA 3 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_457 -x-1,y,-z+2 -1 0 0 0 1 0 0 0 -1 -260.636467 0 439.523377 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 F N N 
? 2 J N N 
? 2 N N N 
? 2 R N N 
? 2 V N N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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 UMP sing 555 n n 
N1 C6 UMP sing 556 n n 
N1 C1' UMP sing 557 n n 
C2 N3 UMP sing 558 n n 
C2 O2 UMP doub 559 n n 
N3 C4 UMP sing 560 n n 
N3 HN3 UMP sing 561 n n 
C4 C5 UMP sing 562 n n 
C4 O4 UMP doub 563 n n 
C5 C6 UMP doub 564 n n 
C5 H5 UMP sing 565 n n 
C6 H6 UMP sing 566 n n 
C1' C2' UMP sing 567 n n 
C1' O4' UMP sing 568 n n 
C1' H1' UMP sing 569 n n 
C2' C3' UMP sing 570 n n 
C2' H2' UMP sing 571 n n 
C2' "H2''" UMP sing 572 n n 
C3' C4' UMP sing 573 n n 
C3' O3' UMP sing 574 n n 
C3' H3' UMP sing 575 n n 
C4' O4' UMP sing 576 n n 
C4' C5' UMP sing 577 n n 
C4' H4' UMP sing 578 n n 
O3' HO3' UMP sing 579 n n 
C5' O5' UMP sing 580 n n 
C5' H5' UMP sing 581 n n 
C5' "H5''" UMP sing 582 n n 
O5' P UMP sing 583 n n 
P OP1 UMP doub 584 n n 
P OP2 UMP sing 585 n n 
P OP3 UMP sing 586 n n 
OP2 HOP2 UMP sing 587 n n 
OP3 HOP3 UMP sing 588 n n 
#
_atom_sites.entry_id                     3DL6 
_atom_sites.fract_transf_matrix[1][1]    0.004653 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000484 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008553 
_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]    0.00455 
_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
F 2 UMP A 1 603 603 UMP UMP . 
G 3 CB3 A 1 604 604 CB3 CB3 . 
H 4 DHF A 1 605 605 DHF DHF . 
I 5 NDP A 1 606 606 NDP NDP . 
J 2 UMP B 1 607 607 UMP UMP . 
K 3 CB3 B 1 608 608 CB3 CB3 . 
L 4 DHF B 1 609 609 DHF DHF . 
M 5 NDP B 1 610 610 NDP NDP . 
N 2 UMP C 1 611 611 UMP UMP . 
O 3 CB3 C 1 612 612 CB3 CB3 . 
P 4 DHF C 1 613 613 DHF DHF . 
Q 5 NDP C 1 614 614 NDP NDP . 
R 2 UMP D 1 615 615 UMP UMP . 
S 3 CB3 D 1 616 616 CB3 CB3 . 
T 4 DHF D 1 617 617 DHF DHF . 
U 5 NDP D 1 618 618 NDP NDP . 
V 2 UMP E 1 619 619 UMP UMP . 
W 3 CB3 E 1 620 620 CB3 CB3 . 
X 4 DHF E 1 621 621 DHF DHF . 
Y 5 NDP E 1 622 622 NDP NDP . 
Z 6 HOH A 1 607 1 HOH HOH . 
Z 6 HOH A 2 608 9 HOH HOH . 
Z 6 HOH A 3 609 10 HOH HOH . 
Z 6 HOH A 4 610 15 HOH HOH . 
Z 6 HOH A 5 611 17 HOH HOH . 
Z 6 HOH A 6 612 19 HOH HOH . 
Z 6 HOH A 7 613 22 HOH HOH . 
Z 6 HOH A 8 614 23 HOH HOH . 
Z 6 HOH A 9 615 25 HOH HOH . 
Z 6 HOH A 10 616 27 HOH HOH . 
Z 6 HOH A 11 617 28 HOH HOH . 
Z 6 HOH A 12 618 29 HOH HOH . 
Z 6 HOH A 13 619 33 HOH HOH . 
Z 6 HOH A 14 620 37 HOH HOH . 
Z 6 HOH A 15 621 47 HOH HOH . 
Z 6 HOH A 16 622 48 HOH HOH . 
Z 6 HOH A 17 623 50 HOH HOH . 
Z 6 HOH A 18 624 58 HOH HOH . 
Z 6 HOH A 19 625 61 HOH HOH . 
Z 6 HOH A 20 626 63 HOH HOH . 
Z 6 HOH A 21 627 64 HOH HOH . 
Z 6 HOH A 22 628 68 HOH HOH . 
Z 6 HOH A 23 629 78 HOH HOH . 
Z 6 HOH A 24 630 101 HOH HOH . 
Z 6 HOH A 25 631 109 HOH HOH . 
Z 6 HOH A 26 632 114 HOH HOH . 
Z 6 HOH A 27 633 117 HOH HOH . 
Z 6 HOH A 28 634 118 HOH HOH . 
Z 6 HOH A 29 635 123 HOH HOH . 
Z 6 HOH A 30 636 126 HOH HOH . 
Z 6 HOH A 31 637 130 HOH HOH . 
Z 6 HOH A 32 638 132 HOH HOH . 
Z 6 HOH A 33 639 141 HOH HOH . 
Z 6 HOH A 34 640 149 HOH HOH . 
Z 6 HOH A 35 641 168 HOH HOH . 
AA 6 HOH B 1 611 3 HOH HOH . 
AA 6 HOH B 2 612 4 HOH HOH . 
AA 6 HOH B 3 613 5 HOH HOH . 
AA 6 HOH B 4 614 8 HOH HOH . 
AA 6 HOH B 5 615 11 HOH HOH . 
AA 6 HOH B 6 616 12 HOH HOH . 
AA 6 HOH B 7 617 13 HOH HOH . 
AA 6 HOH B 8 618 16 HOH HOH . 
AA 6 HOH B 9 619 20 HOH HOH . 
AA 6 HOH B 10 620 24 HOH HOH . 
AA 6 HOH B 11 621 30 HOH HOH . 
AA 6 HOH B 12 622 34 HOH HOH . 
AA 6 HOH B 13 623 35 HOH HOH . 
AA 6 HOH B 14 624 38 HOH HOH . 
AA 6 HOH B 15 625 52 HOH HOH . 
AA 6 HOH B 16 626 53 HOH HOH . 
AA 6 HOH B 17 627 54 HOH HOH . 
AA 6 HOH B 18 628 55 HOH HOH . 
AA 6 HOH B 19 629 57 HOH HOH . 
AA 6 HOH B 20 630 59 HOH HOH . 
AA 6 HOH B 21 631 60 HOH HOH . 
AA 6 HOH B 22 632 65 HOH HOH . 
AA 6 HOH B 23 633 67 HOH HOH . 
AA 6 HOH B 24 634 73 HOH HOH . 
AA 6 HOH B 25 635 74 HOH HOH . 
AA 6 HOH B 26 636 75 HOH HOH . 
AA 6 HOH B 27 637 77 HOH HOH . 
AA 6 HOH B 28 638 79 HOH HOH . 
AA 6 HOH B 29 639 80 HOH HOH . 
AA 6 HOH B 30 640 82 HOH HOH . 
AA 6 HOH B 31 641 87 HOH HOH . 
AA 6 HOH B 32 642 88 HOH HOH . 
AA 6 HOH B 33 643 89 HOH HOH . 
AA 6 HOH B 34 644 91 HOH HOH . 
AA 6 HOH B 35 645 97 HOH HOH . 
AA 6 HOH B 36 646 98 HOH HOH . 
AA 6 HOH B 37 647 103 HOH HOH . 
AA 6 HOH B 38 648 106 HOH HOH . 
AA 6 HOH B 39 649 110 HOH HOH . 
AA 6 HOH B 40 650 119 HOH HOH . 
AA 6 HOH B 41 651 122 HOH HOH . 
AA 6 HOH B 42 652 127 HOH HOH . 
AA 6 HOH B 43 653 136 HOH HOH . 
AA 6 HOH B 44 654 139 HOH HOH . 
AA 6 HOH B 45 655 146 HOH HOH . 
AA 6 HOH B 46 656 152 HOH HOH . 
AA 6 HOH B 47 657 155 HOH HOH . 
AA 6 HOH B 48 658 159 HOH HOH . 
BA 6 HOH C 1 615 7 HOH HOH . 
BA 6 HOH C 2 616 18 HOH HOH . 
BA 6 HOH C 3 617 21 HOH HOH . 
BA 6 HOH C 4 618 26 HOH HOH . 
BA 6 HOH C 5 619 45 HOH HOH . 
BA 6 HOH C 6 620 46 HOH HOH . 
BA 6 HOH C 7 621 51 HOH HOH . 
BA 6 HOH C 8 622 62 HOH HOH . 
BA 6 HOH C 9 623 66 HOH HOH . 
BA 6 HOH C 10 624 81 HOH HOH . 
BA 6 HOH C 11 625 104 HOH HOH . 
BA 6 HOH C 12 626 105 HOH HOH . 
BA 6 HOH C 13 627 108 HOH HOH . 
BA 6 HOH C 14 628 120 HOH HOH . 
BA 6 HOH C 15 629 124 HOH HOH . 
BA 6 HOH C 16 630 125 HOH HOH . 
BA 6 HOH C 17 631 131 HOH HOH . 
BA 6 HOH C 18 632 134 HOH HOH . 
BA 6 HOH C 19 633 135 HOH HOH . 
BA 6 HOH C 20 634 137 HOH HOH . 
BA 6 HOH C 21 635 140 HOH HOH . 
BA 6 HOH C 22 636 164 HOH HOH . 
CA 6 HOH D 1 619 2 HOH HOH . 
CA 6 HOH D 2 620 31 HOH HOH . 
CA 6 HOH D 3 621 32 HOH HOH . 
CA 6 HOH D 4 622 40 HOH HOH . 
CA 6 HOH D 5 623 41 HOH HOH . 
CA 6 HOH D 6 624 42 HOH HOH . 
CA 6 HOH D 7 625 44 HOH HOH . 
CA 6 HOH D 8 626 56 HOH HOH . 
CA 6 HOH D 9 627 69 HOH HOH . 
CA 6 HOH D 10 628 70 HOH HOH . 
CA 6 HOH D 11 629 84 HOH HOH . 
CA 6 HOH D 12 630 90 HOH HOH . 
CA 6 HOH D 13 631 92 HOH HOH . 
CA 6 HOH D 14 632 94 HOH HOH . 
CA 6 HOH D 15 633 102 HOH HOH . 
CA 6 HOH D 16 634 113 HOH HOH . 
CA 6 HOH D 17 635 121 HOH HOH . 
CA 6 HOH D 18 636 128 HOH HOH . 
CA 6 HOH D 19 637 133 HOH HOH . 
CA 6 HOH D 20 638 144 HOH HOH . 
CA 6 HOH D 21 639 145 HOH HOH . 
CA 6 HOH D 22 640 167 HOH HOH . 
CA 6 HOH D 23 641 172 HOH HOH . 
DA 6 HOH E 1 623 6 HOH HOH . 
DA 6 HOH E 2 624 14 HOH HOH . 
DA 6 HOH E 3 625 36 HOH HOH . 
DA 6 HOH E 4 626 49 HOH HOH . 
DA 6 HOH E 5 627 71 HOH HOH . 
DA 6 HOH E 6 628 72 HOH HOH . 
DA 6 HOH E 7 629 76 HOH HOH . 
DA 6 HOH E 8 630 83 HOH HOH . 
DA 6 HOH E 9 631 85 HOH HOH . 
DA 6 HOH E 10 632 95 HOH HOH . 
DA 6 HOH E 11 633 99 HOH HOH . 
DA 6 HOH E 12 634 100 HOH HOH . 
DA 6 HOH E 13 635 111 HOH HOH . 
DA 6 HOH E 14 636 129 HOH HOH . 
DA 6 HOH E 15 637 156 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 UMP . . . R 2 -101.598 140.572 65.091 1 63.66 ? N1 UMP 615 D 1 
HETATM 2 C C2 UMP . . . R 2 -100.204 140.614 64.944 1 63.66 ? C2 UMP 615 D 1 
HETATM 3 N N3 UMP . . . R 2 -99.361 140.154 65.963 1 63.66 ? N3 UMP 615 D 1 
HETATM 4 C C4 UMP . . . R 2 -99.841 139.96 67.263 1 63.66 ? C4 UMP 615 D 1 
HETATM 5 C C5 UMP . . . R 2 -101.292 140.326 67.588 1 63.66 ? C5 UMP 615 D 1 
HETATM 6 C C6 UMP . . . R 2 -102.22 140.18 66.378 1 63.66 ? C6 UMP 615 D 1 
HETATM 7 O O2 UMP . . . R 2 -99.731 140.83 63.831 1 84.5 ? O2 UMP 615 D 1 
HETATM 8 O O4 UMP . . . R 2 -99.104 139.465 68.116 1 65.78 ? O4 UMP 615 D 1 
HETATM 9 C C1' UMP . . . R 2 -102.459 140.788 63.901 1 63.66 ? C1' UMP 615 D 1 
HETATM 10 C C2' UMP . . . R 2 -102.145 139.814 62.763 1 63.66 ? C2' UMP 615 D 1 
HETATM 11 C C3' UMP . . . R 2 -103.433 139.933 61.95 1 63.66 ? C3' UMP 615 D 1 
HETATM 12 C C4' UMP . . . R 2 -104.465 139.892 63.078 1 63.66 ? C4' UMP 615 D 1 
HETATM 13 O O3' UMP . . . R 2 -103.512 141.197 61.286 1 65.71 ? O3' UMP 615 D 1 
HETATM 14 O O4' UMP . . . R 2 -103.851 140.565 64.19 1 62.14 ? O4' UMP 615 D 1 
HETATM 15 C C5' UMP . . . R 2 -104.761 138.445 63.481 1 63.66 ? C5' UMP 615 D 1 
HETATM 16 O O5' UMP . . . R 2 -106.093 138.099 63.094 1 59.6 ? O5' UMP 615 D 1 
HETATM 17 P P UMP . . . R 2 -106.392 136.755 62.263 1 63.66 ? P UMP 615 D 1 
HETATM 18 O OP1 UMP . . . R 2 -107.366 135.869 62.932 1 57.42 ? OP1 UMP 615 D 1 
HETATM 19 O OP2 UMP . . . R 2 -106.918 137.218 60.816 1 57.18 ? OP2 UMP 615 D 1 
HETATM 20 O OP3 UMP . . . R 2 -104.986 136.015 62.02 1 60.23 ? OP3 UMP 615 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           20 
#