data_1JY8
#
_model_server_result.job_id            zchYOumYEDBGuOhLJzstYg 
_model_server_result.datetime_utc      '2024-11-24 13:35:31' 
_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          1jy8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":669}' 
#
_entry.id    1JY8 
#
_exptl.entry_id    1JY8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.197 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-MONOPHOSPHATE" 
_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            1JY8 
_cell.length_a            144.63 
_cell.length_b            144.63 
_cell.length_c            144.63 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JY8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 A OD1 ASP 8 A ASP 8 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc2 A NE2 HIS 10 A HIS 10 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc3 A ND1 HIS 42 A HIS 42 1_555 B ZN ZN . A ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc4 B ZN ZN . A ZN 300 1_555 D OA2 CDI . A CDI 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
#
_chem_comp.formula           'C9 H14 N3 O8 P' 
_chem_comp.formula_weight    323.197 
_chem_comp.id                C5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
O3P P C5P sing 70 n n 
O3P HOP3 C5P sing 71 n n 
P O1P C5P doub 72 n n 
P O2P C5P sing 73 n n 
P O5' C5P sing 74 n n 
O2P HOP2 C5P sing 75 n n 
O5' C5' C5P sing 76 n n 
C5' C4' C5P sing 77 n n 
C5' "H5'1" C5P sing 78 n n 
C5' "H5'2" C5P sing 79 n n 
C4' O4' C5P sing 80 n n 
C4' C3' C5P sing 81 n n 
C4' H4' C5P sing 82 n n 
O4' C1' C5P sing 83 n n 
C3' O3' C5P sing 84 n n 
C3' C2' C5P sing 85 n n 
C3' H3' C5P sing 86 n n 
O3' HO3' C5P sing 87 n n 
C2' O2' C5P sing 88 n n 
C2' C1' C5P sing 89 n n 
C2' "H2'1" C5P sing 90 n n 
O2' HO2' C5P sing 91 n n 
C1' N1 C5P sing 92 n n 
C1' H1' C5P sing 93 n n 
N1 C2 C5P sing 94 n n 
N1 C6 C5P sing 95 n n 
C2 N3 C5P sing 96 n n 
C2 O2 C5P doub 97 n n 
N3 C4 C5P doub 98 n n 
C4 C5 C5P sing 99 n n 
C4 N4 C5P sing 100 n n 
C5 C6 C5P doub 101 n n 
C5 H5 C5P sing 102 n n 
C6 H6 C5P sing 103 n n 
N4 HN41 C5P sing 104 n n 
N4 HN42 C5P sing 105 n n 
#
_atom_sites.entry_id                     1JY8 
_atom_sites.fract_transf_matrix[1][1]    0.006914 
_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]    0.006914 
_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]    0.006914 
_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 ZN A 1 300 300 ZN ZN . 
C 3 C5P A 1 669 669 C5P CMP . 
D 4 CDI A 1 421 421 CDI CDI . 
E 5 HOH A 1 500 500 HOH SOL . 
E 5 HOH A 2 501 501 HOH SOL . 
E 5 HOH A 3 502 502 HOH SOL . 
E 5 HOH A 4 504 504 HOH SOL . 
E 5 HOH A 5 506 506 HOH SOL . 
E 5 HOH A 6 507 507 HOH SOL . 
E 5 HOH A 7 509 509 HOH SOL . 
E 5 HOH A 8 510 510 HOH SOL . 
E 5 HOH A 9 511 511 HOH SOL . 
E 5 HOH A 10 512 512 HOH SOL . 
E 5 HOH A 11 513 513 HOH SOL . 
E 5 HOH A 12 514 514 HOH SOL . 
E 5 HOH A 13 515 515 HOH SOL . 
E 5 HOH A 14 516 516 HOH SOL . 
E 5 HOH A 15 517 517 HOH SOL . 
E 5 HOH A 16 518 518 HOH SOL . 
E 5 HOH A 17 519 519 HOH SOL . 
E 5 HOH A 18 520 520 HOH SOL . 
E 5 HOH A 19 521 521 HOH SOL . 
E 5 HOH A 20 523 523 HOH SOL . 
E 5 HOH A 21 524 524 HOH SOL . 
E 5 HOH A 22 525 525 HOH SOL . 
E 5 HOH A 23 526 526 HOH SOL . 
E 5 HOH A 24 527 527 HOH SOL . 
E 5 HOH A 25 528 528 HOH SOL . 
E 5 HOH A 26 529 529 HOH SOL . 
E 5 HOH A 27 530 530 HOH SOL . 
E 5 HOH A 28 531 531 HOH SOL . 
E 5 HOH A 29 532 532 HOH SOL . 
E 5 HOH A 30 533 533 HOH SOL . 
E 5 HOH A 31 535 535 HOH SOL . 
E 5 HOH A 32 536 536 HOH SOL . 
E 5 HOH A 33 537 537 HOH SOL . 
E 5 HOH A 34 538 538 HOH SOL . 
E 5 HOH A 35 539 539 HOH SOL . 
E 5 HOH A 36 540 540 HOH SOL . 
E 5 HOH A 37 541 541 HOH SOL . 
E 5 HOH A 38 542 542 HOH SOL . 
E 5 HOH A 39 543 543 HOH SOL . 
E 5 HOH A 40 545 545 HOH SOL . 
E 5 HOH A 41 546 546 HOH SOL . 
E 5 HOH A 42 547 547 HOH SOL . 
E 5 HOH A 43 549 549 HOH SOL . 
E 5 HOH A 44 550 550 HOH SOL . 
E 5 HOH A 45 551 551 HOH SOL . 
E 5 HOH A 46 554 554 HOH SOL . 
E 5 HOH A 47 555 555 HOH SOL . 
E 5 HOH A 48 556 556 HOH SOL . 
E 5 HOH A 49 557 557 HOH SOL . 
E 5 HOH A 50 558 558 HOH SOL . 
E 5 HOH A 51 560 560 HOH SOL . 
E 5 HOH A 52 561 561 HOH SOL . 
E 5 HOH A 53 563 563 HOH SOL . 
E 5 HOH A 54 564 564 HOH SOL . 
E 5 HOH A 55 568 568 HOH SOL . 
E 5 HOH A 56 571 571 HOH SOL . 
E 5 HOH A 57 573 573 HOH SOL . 
E 5 HOH A 58 574 574 HOH SOL . 
E 5 HOH A 59 575 575 HOH SOL . 
E 5 HOH A 60 576 576 HOH SOL . 
E 5 HOH A 61 579 579 HOH SOL . 
E 5 HOH A 62 580 580 HOH SOL . 
E 5 HOH A 63 581 581 HOH SOL . 
E 5 HOH A 64 582 582 HOH SOL . 
E 5 HOH A 65 583 583 HOH SOL . 
E 5 HOH A 66 584 584 HOH SOL . 
E 5 HOH A 67 585 585 HOH SOL . 
E 5 HOH A 68 586 586 HOH SOL . 
E 5 HOH A 69 588 588 HOH SOL . 
E 5 HOH A 70 589 589 HOH SOL . 
E 5 HOH A 71 590 590 HOH SOL . 
E 5 HOH A 72 592 592 HOH SOL . 
#
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 O O3P C5P . . . C 3 13.284 28.723 8.646 1 55.89 ? O3P C5P 669 A 1 
HETATM 2 P P C5P . . . C 3 11.617 28.833 8.56 1 50.19 ? P C5P 669 A 1 
HETATM 3 O O1P C5P . . . C 3 10.986 27.655 9.312 1 52.54 ? O1P C5P 669 A 1 
HETATM 4 O O2P C5P . . . C 3 11.145 28.834 7.095 1 52.9 ? O2P C5P 669 A 1 
HETATM 5 O O5' C5P . . . C 3 11.092 30.258 9.238 1 50.1 ? O5' C5P 669 A 1 
HETATM 6 C C5' C5P . . . C 3 11.944 31.083 10.034 1 45.34 ? C5' C5P 669 A 1 
HETATM 7 C C4' C5P . . . C 3 11.109 32.098 10.704 1 46.43 ? C4' C5P 669 A 1 
HETATM 8 O O4' C5P . . . C 3 9.73 31.773 10.761 1 44.13 ? O4' C5P 669 A 1 
HETATM 9 C C3' C5P . . . C 3 11.581 32.008 12.165 1 46.95 ? C3' C5P 669 A 1 
HETATM 10 O O3' C5P . . . C 3 11.914 33.315 12.497 1 47.32 ? O3' C5P 669 A 1 
HETATM 11 C C2' C5P . . . C 3 10.38 31.568 12.97 1 47.77 ? C2' C5P 669 A 1 
HETATM 12 O O2' C5P . . . C 3 10.165 32.303 14.186 1 51.39 ? O2' C5P 669 A 1 
HETATM 13 C C1' C5P . . . C 3 9.234 31.805 12.05 1 42.58 ? C1' C5P 669 A 1 
HETATM 14 N N1 C5P . . . C 3 8.686 30.549 12.364 1 38.4 ? N1 C5P 669 A 1 
HETATM 15 C C2 C5P . . . C 3 7.627 30.697 13.28 1 35.68 ? C2 C5P 669 A 1 
HETATM 16 N N3 C5P . . . C 3 6.891 29.641 13.732 1 33.85 ? N3 C5P 669 A 1 
HETATM 17 C C4 C5P . . . C 3 7.163 28.402 13.299 1 31.3 ? C4 C5P 669 A 1 
HETATM 18 C C5 C5P . . . C 3 8.196 28.191 12.4 1 31.13 ? C5 C5P 669 A 1 
HETATM 19 C C6 C5P . . . C 3 8.922 29.286 11.968 1 34.57 ? C6 C5P 669 A 1 
HETATM 20 O O2 C5P . . . C 3 7.284 31.799 13.74 1 36.82 ? O2 C5P 669 A 1 
HETATM 21 N N4 C5P . . . C 3 6.423 27.394 13.748 1 29.67 ? N4 C5P 669 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#