data_2BBQ
#
_model_server_result.job_id            rd_ICPKUPSZH_ino4siE3g 
_model_server_result.datetime_utc      '2024-10-19 16:29:31' 
_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          2bbq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":530}' 
#
_entry.id    2BBQ 
#
_exptl.entry_id    2BBQ 
_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    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            2BBQ 
_cell.length_a            127.1 
_cell.length_b            127.1 
_cell.length_c            67.9 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2BBQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63' 
#
_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 
_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
? 2 C N N 
? 2 E N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? 
covale ? covale2 B SG CYS 146 B CYS 146 1_555 E C6 UMP . B UMP 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
#
_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 466 n n 
N1 C6 UMP sing 467 n n 
N1 C1' UMP sing 468 n n 
C2 N3 UMP sing 469 n n 
C2 O2 UMP doub 470 n n 
N3 C4 UMP sing 471 n n 
N3 HN3 UMP sing 472 n n 
C4 C5 UMP sing 473 n n 
C4 O4 UMP doub 474 n n 
C5 C6 UMP doub 475 n n 
C5 H5 UMP sing 476 n n 
C6 H6 UMP sing 477 n n 
C1' C2' UMP sing 478 n n 
C1' O4' UMP sing 479 n n 
C1' H1' UMP sing 480 n n 
C2' C3' UMP sing 481 n n 
C2' H2' UMP sing 482 n n 
C2' "H2''" UMP sing 483 n n 
C3' C4' UMP sing 484 n n 
C3' O3' UMP sing 485 n n 
C3' H3' UMP sing 486 n n 
C4' O4' UMP sing 487 n n 
C4' C5' UMP sing 488 n n 
C4' H4' UMP sing 489 n n 
O3' HO3' UMP sing 490 n n 
C5' O5' UMP sing 491 n n 
C5' H5' UMP sing 492 n n 
C5' "H5''" UMP sing 493 n n 
O5' P UMP sing 494 n n 
P OP1 UMP doub 495 n n 
P OP2 UMP sing 496 n n 
P OP3 UMP sing 497 n n 
OP2 HOP2 UMP sing 498 n n 
OP3 HOP3 UMP sing 499 n n 
#
_atom_sites.entry_id                     2BBQ 
_atom_sites.fract_transf_matrix[1][1]    0.007868 
_atom_sites.fract_transf_matrix[1][2]    0.004542 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009085 
_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]    0.014728 
_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 UMP A 1 529 529 UMP UMP . 
D 3 PFG A 1 531 531 PFG PFG . 
E 2 UMP B 1 530 530 UMP UMP . 
F 3 PFG B 1 532 532 PFG PFG . 
G 4 HOH A 1 532 2 HOH HOH . 
G 4 HOH A 2 533 3 HOH HOH . 
G 4 HOH A 3 534 4 HOH HOH . 
G 4 HOH A 4 535 5 HOH HOH . 
G 4 HOH A 5 536 6 HOH HOH . 
G 4 HOH A 6 537 8 HOH HOH . 
G 4 HOH A 7 538 9 HOH HOH . 
G 4 HOH A 8 539 10 HOH HOH . 
G 4 HOH A 9 540 15 HOH HOH . 
G 4 HOH A 10 541 16 HOH HOH . 
G 4 HOH A 11 542 17 HOH HOH . 
G 4 HOH A 12 543 19 HOH HOH . 
G 4 HOH A 13 544 20 HOH HOH . 
G 4 HOH A 14 545 21 HOH HOH . 
G 4 HOH A 15 546 22 HOH HOH . 
G 4 HOH A 16 547 23 HOH HOH . 
G 4 HOH A 17 548 24 HOH HOH . 
G 4 HOH A 18 549 25 HOH HOH . 
G 4 HOH A 19 550 26 HOH HOH . 
G 4 HOH A 20 551 28 HOH HOH . 
G 4 HOH A 21 552 29 HOH HOH . 
G 4 HOH A 22 553 30 HOH HOH . 
G 4 HOH A 23 554 31 HOH HOH . 
G 4 HOH A 24 555 33 HOH HOH . 
G 4 HOH A 25 556 35 HOH HOH . 
G 4 HOH A 26 557 36 HOH HOH . 
G 4 HOH A 27 558 37 HOH HOH . 
G 4 HOH A 28 559 38 HOH HOH . 
G 4 HOH A 29 560 39 HOH HOH . 
G 4 HOH A 30 561 40 HOH HOH . 
G 4 HOH A 31 562 41 HOH HOH . 
G 4 HOH A 32 563 42 HOH HOH . 
G 4 HOH A 33 564 43 HOH HOH . 
G 4 HOH A 34 565 44 HOH HOH . 
G 4 HOH A 35 566 45 HOH HOH . 
G 4 HOH A 36 567 46 HOH HOH . 
G 4 HOH A 37 568 47 HOH HOH . 
G 4 HOH A 38 569 48 HOH HOH . 
G 4 HOH A 39 570 49 HOH HOH . 
G 4 HOH A 40 571 50 HOH HOH . 
G 4 HOH A 41 572 51 HOH HOH . 
G 4 HOH A 42 573 52 HOH HOH . 
G 4 HOH A 43 574 53 HOH HOH . 
G 4 HOH A 44 575 54 HOH HOH . 
G 4 HOH A 45 576 55 HOH HOH . 
G 4 HOH A 46 577 57 HOH HOH . 
G 4 HOH A 47 578 58 HOH HOH . 
G 4 HOH A 48 579 59 HOH HOH . 
G 4 HOH A 49 580 61 HOH HOH . 
G 4 HOH A 50 581 64 HOH HOH . 
G 4 HOH A 51 582 65 HOH HOH . 
G 4 HOH A 52 583 66 HOH HOH . 
G 4 HOH A 53 584 68 HOH HOH . 
G 4 HOH A 54 585 69 HOH HOH . 
G 4 HOH A 55 586 74 HOH HOH . 
G 4 HOH A 56 587 77 HOH HOH . 
G 4 HOH A 57 588 80 HOH HOH . 
G 4 HOH A 58 589 81 HOH HOH . 
G 4 HOH A 59 590 83 HOH HOH . 
G 4 HOH A 60 591 88 HOH HOH . 
G 4 HOH A 61 592 90 HOH HOH . 
G 4 HOH A 62 593 91 HOH HOH . 
G 4 HOH A 63 594 92 HOH HOH . 
G 4 HOH A 64 595 93 HOH HOH . 
G 4 HOH A 65 596 101 HOH HOH . 
G 4 HOH A 66 597 103 HOH HOH . 
G 4 HOH A 67 598 104 HOH HOH . 
H 4 HOH B 1 533 1 HOH HOH . 
H 4 HOH B 2 534 7 HOH HOH . 
H 4 HOH B 3 535 11 HOH HOH . 
H 4 HOH B 4 536 12 HOH HOH . 
H 4 HOH B 5 537 13 HOH HOH . 
H 4 HOH B 6 538 14 HOH HOH . 
H 4 HOH B 7 539 18 HOH HOH . 
H 4 HOH B 8 540 27 HOH HOH . 
H 4 HOH B 9 541 32 HOH HOH . 
H 4 HOH B 10 542 34 HOH HOH . 
H 4 HOH B 11 543 56 HOH HOH . 
H 4 HOH B 12 544 60 HOH HOH . 
H 4 HOH B 13 545 62 HOH HOH . 
H 4 HOH B 14 546 63 HOH HOH . 
H 4 HOH B 15 547 67 HOH HOH . 
H 4 HOH B 16 548 70 HOH HOH . 
H 4 HOH B 17 549 71 HOH HOH . 
H 4 HOH B 18 550 72 HOH HOH . 
H 4 HOH B 19 551 73 HOH HOH . 
H 4 HOH B 20 552 75 HOH HOH . 
H 4 HOH B 21 553 76 HOH HOH . 
H 4 HOH B 22 554 78 HOH HOH . 
H 4 HOH B 23 555 79 HOH HOH . 
H 4 HOH B 24 556 82 HOH HOH . 
H 4 HOH B 25 557 84 HOH HOH . 
H 4 HOH B 26 558 85 HOH HOH . 
H 4 HOH B 27 559 86 HOH HOH . 
H 4 HOH B 28 560 87 HOH HOH . 
H 4 HOH B 29 561 89 HOH HOH . 
H 4 HOH B 30 562 94 HOH HOH . 
H 4 HOH B 31 563 95 HOH HOH . 
H 4 HOH B 32 564 96 HOH HOH . 
H 4 HOH B 33 565 97 HOH HOH . 
H 4 HOH B 34 566 98 HOH HOH . 
H 4 HOH B 35 567 99 HOH HOH . 
H 4 HOH B 36 568 100 HOH HOH . 
H 4 HOH B 37 569 102 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 . . . E 2 43.875 34.229 24.506 1 12.05 ? N1 UMP 530 B 1 
HETATM 2 C C2 UMP . . . E 2 43.098 35.123 25.204 1 9.61 ? C2 UMP 530 B 1 
HETATM 3 N N3 UMP . . . E 2 42.066 35.699 24.457 1 12.9 ? N3 UMP 530 B 1 
HETATM 4 C C4 UMP . . . E 2 41.917 35.655 23.055 1 13.81 ? C4 UMP 530 B 1 
HETATM 5 C C5 UMP . . . E 2 42.928 34.832 22.345 1 14.94 ? C5 UMP 530 B 1 
HETATM 6 C C6 UMP . . . E 2 43.375 33.724 23.23 1 13.94 ? C6 UMP 530 B 1 
HETATM 7 O O2 UMP . . . E 2 43.234 35.332 26.408 1 4.17 ? O2 UMP 530 B 1 
HETATM 8 O O4 UMP . . . E 2 40.939 36.179 22.5 1 15.3 ? O4 UMP 530 B 1 
HETATM 9 C C1' UMP . . . E 2 45.054 33.585 25.004 1 13.21 ? C1' UMP 530 B 1 
HETATM 10 C C2' UMP . . . E 2 45.131 32.788 26.314 1 14.6 ? C2' UMP 530 B 1 
HETATM 11 C C3' UMP . . . E 2 46.48 32.081 26.29 1 11.35 ? C3' UMP 530 B 1 
HETATM 12 C C4' UMP . . . E 2 46.818 32.071 24.793 1 12.97 ? C4' UMP 530 B 1 
HETATM 13 O O3' UMP . . . E 2 47.374 32.938 26.979 1 16.07 ? O3' UMP 530 B 1 
HETATM 14 O O4' UMP . . . E 2 46.222 33.291 24.233 1 15.35 ? O4' UMP 530 B 1 
HETATM 15 C C5' UMP . . . E 2 46.226 30.887 24.04 1 5.83 ? C5' UMP 530 B 1 
HETATM 16 O O5' UMP . . . E 2 47.096 29.754 24.274 1 11.94 ? O5' UMP 530 B 1 
HETATM 17 P P UMP . . . E 2 46.464 28.316 24.497 1 7.56 ? P UMP 530 B 1 
HETATM 18 O OP1 UMP . . . E 2 45.537 28.459 25.614 1 15.46 ? OP1 UMP 530 B 1 
HETATM 19 O OP2 UMP . . . E 2 45.728 27.863 23.284 1 9.78 ? OP2 UMP 530 B 1 
HETATM 20 O OP3 UMP . . . E 2 47.468 27.333 24.873 1 14.16 ? OP3 UMP 530 B 1 
#
_model_server_stats.io_time_ms              79 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#