data_5B6E
#
_model_server_result.job_id            H1LujXEcEXFvRYejdFtj6w 
_model_server_result.datetime_utc      '2024-11-08 07:37:22' 
_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          5b6e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    5B6E 
#
_exptl.entry_id    5B6E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              353.223 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" 
_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            5B6E 
_cell.length_a            109.323 
_cell.length_b            109.323 
_cell.length_c            112.867 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5B6E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_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 
_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 D N N 
#
_chem_comp.formula           'C10 H16 N3 O9 P' 
_chem_comp.formula_weight    353.223 
_chem_comp.id                5HM 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     "5-hydroxymethylcytidine 5'-monophosphate" 
#
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
N4 C4 5HM sing 1 n n 
C4 N3 5HM doub 2 n n 
C4 C5 5HM sing 3 n n 
N3 C2 5HM sing 4 n n 
CM5 OM5 5HM sing 5 n n 
CM5 C5 5HM sing 6 n n 
C5 C6 5HM doub 7 n n 
C2 O2 5HM doub 8 n n 
C2 N1 5HM sing 9 n n 
C6 N1 5HM sing 10 n n 
N1 C1' 5HM sing 11 n n 
OP1 P 5HM doub 12 n n 
C1' O4' 5HM sing 13 n n 
C1' C2' 5HM sing 14 n n 
OP2 P 5HM sing 15 n n 
O4' C4' 5HM sing 16 n n 
C2' O2' 5HM sing 17 n n 
C2' C3' 5HM sing 18 n n 
P O5' 5HM sing 19 n n 
P OP3 5HM sing 20 n n 
O5' C5' 5HM sing 21 n n 
C5' C4' 5HM sing 22 n n 
C4' C3' 5HM sing 23 n n 
C3' O3' 5HM sing 24 n n 
OP3 H1 5HM sing 25 n n 
OP2 H2 5HM sing 26 n n 
C5' H3 5HM sing 27 n n 
C5' H4 5HM sing 28 n n 
C4' H5 5HM sing 29 n n 
C3' H6 5HM sing 30 n n 
O3' HO3' 5HM sing 31 n n 
C2' H8 5HM sing 32 n n 
O2' H9 5HM sing 33 n n 
C1' H10 5HM sing 34 n n 
C6 H11 5HM sing 35 n n 
CM5 H12 5HM sing 36 n n 
CM5 H13 5HM sing 37 n n 
OM5 H14 5HM sing 38 n n 
N4 H15 5HM sing 39 n n 
N4 H16 5HM sing 40 n n 
#
_atom_sites.entry_id                     5B6E 
_atom_sites.fract_transf_matrix[1][1]    0.009147 
_atom_sites.fract_transf_matrix[1][2]    0.005281 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010562 
_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]    0.00886 
_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 5HM A 1 401 2 5HM 5HC . 
D 2 5HM B 1 401 1 5HM 5HC . 
E 3 HOH A 1 501 16 HOH HOH . 
E 3 HOH A 2 502 155 HOH HOH . 
E 3 HOH A 3 503 47 HOH HOH . 
E 3 HOH A 4 504 55 HOH HOH . 
E 3 HOH A 5 505 62 HOH HOH . 
E 3 HOH A 6 506 41 HOH HOH . 
E 3 HOH A 7 507 185 HOH HOH . 
E 3 HOH A 8 508 170 HOH HOH . 
E 3 HOH A 9 509 128 HOH HOH . 
E 3 HOH A 10 510 36 HOH HOH . 
E 3 HOH A 11 511 79 HOH HOH . 
E 3 HOH A 12 512 23 HOH HOH . 
E 3 HOH A 13 513 127 HOH HOH . 
E 3 HOH A 14 514 97 HOH HOH . 
E 3 HOH A 15 515 138 HOH HOH . 
E 3 HOH A 16 516 42 HOH HOH . 
E 3 HOH A 17 517 20 HOH HOH . 
E 3 HOH A 18 518 30 HOH HOH . 
E 3 HOH A 19 519 11 HOH HOH . 
E 3 HOH A 20 520 141 HOH HOH . 
E 3 HOH A 21 521 43 HOH HOH . 
E 3 HOH A 22 522 8 HOH HOH . 
E 3 HOH A 23 523 12 HOH HOH . 
E 3 HOH A 24 524 61 HOH HOH . 
E 3 HOH A 25 525 129 HOH HOH . 
E 3 HOH A 26 526 193 HOH HOH . 
E 3 HOH A 27 527 92 HOH HOH . 
E 3 HOH A 28 528 94 HOH HOH . 
E 3 HOH A 29 529 150 HOH HOH . 
E 3 HOH A 30 530 15 HOH HOH . 
E 3 HOH A 31 531 89 HOH HOH . 
E 3 HOH A 32 532 191 HOH HOH . 
E 3 HOH A 33 533 125 HOH HOH . 
E 3 HOH A 34 534 101 HOH HOH . 
E 3 HOH A 35 535 56 HOH HOH . 
E 3 HOH A 36 536 50 HOH HOH . 
E 3 HOH A 37 537 84 HOH HOH . 
E 3 HOH A 38 538 44 HOH HOH . 
E 3 HOH A 39 539 21 HOH HOH . 
E 3 HOH A 40 540 22 HOH HOH . 
E 3 HOH A 41 541 93 HOH HOH . 
E 3 HOH A 42 542 147 HOH HOH . 
E 3 HOH A 43 543 103 HOH HOH . 
E 3 HOH A 44 544 148 HOH HOH . 
E 3 HOH A 45 545 91 HOH HOH . 
E 3 HOH A 46 546 66 HOH HOH . 
E 3 HOH A 47 547 105 HOH HOH . 
E 3 HOH A 48 548 5 HOH HOH . 
E 3 HOH A 49 549 179 HOH HOH . 
E 3 HOH A 50 550 40 HOH HOH . 
E 3 HOH A 51 551 196 HOH HOH . 
E 3 HOH A 52 552 175 HOH HOH . 
E 3 HOH A 53 553 25 HOH HOH . 
E 3 HOH A 54 554 76 HOH HOH . 
E 3 HOH A 55 555 64 HOH HOH . 
E 3 HOH A 56 556 48 HOH HOH . 
E 3 HOH A 57 557 13 HOH HOH . 
E 3 HOH A 58 558 188 HOH HOH . 
E 3 HOH A 59 559 107 HOH HOH . 
E 3 HOH A 60 560 18 HOH HOH . 
E 3 HOH A 61 561 137 HOH HOH . 
E 3 HOH A 62 562 49 HOH HOH . 
E 3 HOH A 63 563 121 HOH HOH . 
E 3 HOH A 64 564 9 HOH HOH . 
E 3 HOH A 65 565 80 HOH HOH . 
E 3 HOH A 66 566 87 HOH HOH . 
E 3 HOH A 67 567 199 HOH HOH . 
E 3 HOH A 68 568 122 HOH HOH . 
E 3 HOH A 69 569 72 HOH HOH . 
E 3 HOH A 70 570 159 HOH HOH . 
E 3 HOH A 71 571 109 HOH HOH . 
E 3 HOH A 72 572 143 HOH HOH . 
E 3 HOH A 73 573 142 HOH HOH . 
E 3 HOH A 74 574 140 HOH HOH . 
E 3 HOH A 75 575 131 HOH HOH . 
E 3 HOH A 76 576 110 HOH HOH . 
E 3 HOH A 77 577 126 HOH HOH . 
E 3 HOH A 78 578 133 HOH HOH . 
E 3 HOH A 79 579 186 HOH HOH . 
E 3 HOH A 80 580 27 HOH HOH . 
E 3 HOH A 81 581 119 HOH HOH . 
E 3 HOH A 82 582 113 HOH HOH . 
E 3 HOH A 83 583 182 HOH HOH . 
E 3 HOH A 84 584 29 HOH HOH . 
E 3 HOH A 85 585 164 HOH HOH . 
E 3 HOH A 86 586 24 HOH HOH . 
E 3 HOH A 87 587 116 HOH HOH . 
E 3 HOH A 88 588 154 HOH HOH . 
E 3 HOH A 89 589 99 HOH HOH . 
E 3 HOH A 90 590 184 HOH HOH . 
E 3 HOH A 91 591 39 HOH HOH . 
E 3 HOH A 92 592 58 HOH HOH . 
E 3 HOH A 93 593 71 HOH HOH . 
E 3 HOH A 94 594 192 HOH HOH . 
E 3 HOH A 95 595 130 HOH HOH . 
E 3 HOH A 96 596 135 HOH HOH . 
E 3 HOH A 97 597 38 HOH HOH . 
E 3 HOH A 98 598 152 HOH HOH . 
E 3 HOH A 99 599 177 HOH HOH . 
E 3 HOH A 100 600 96 HOH HOH . 
E 3 HOH A 101 601 163 HOH HOH . 
E 3 HOH A 102 602 2 HOH HOH . 
E 3 HOH A 103 603 201 HOH HOH . 
E 3 HOH A 104 604 197 HOH HOH . 
E 3 HOH A 105 605 3 HOH HOH . 
E 3 HOH A 106 606 26 HOH HOH . 
E 3 HOH A 107 607 1 HOH HOH . 
E 3 HOH A 108 608 169 HOH HOH . 
E 3 HOH A 109 609 200 HOH HOH . 
E 3 HOH A 110 610 172 HOH HOH . 
E 3 HOH A 111 611 198 HOH HOH . 
F 3 HOH B 1 501 100 HOH HOH . 
F 3 HOH B 2 502 183 HOH HOH . 
F 3 HOH B 3 503 78 HOH HOH . 
F 3 HOH B 4 504 57 HOH HOH . 
F 3 HOH B 5 505 90 HOH HOH . 
F 3 HOH B 6 506 59 HOH HOH . 
F 3 HOH B 7 507 67 HOH HOH . 
F 3 HOH B 8 508 10 HOH HOH . 
F 3 HOH B 9 509 17 HOH HOH . 
F 3 HOH B 10 510 194 HOH HOH . 
F 3 HOH B 11 511 65 HOH HOH . 
F 3 HOH B 12 512 45 HOH HOH . 
F 3 HOH B 13 513 85 HOH HOH . 
F 3 HOH B 14 514 31 HOH HOH . 
F 3 HOH B 15 515 98 HOH HOH . 
F 3 HOH B 16 516 7 HOH HOH . 
F 3 HOH B 17 517 6 HOH HOH . 
F 3 HOH B 18 518 111 HOH HOH . 
F 3 HOH B 19 519 139 HOH HOH . 
F 3 HOH B 20 520 68 HOH HOH . 
F 3 HOH B 21 521 132 HOH HOH . 
F 3 HOH B 22 522 82 HOH HOH . 
F 3 HOH B 23 523 4 HOH HOH . 
F 3 HOH B 24 524 37 HOH HOH . 
F 3 HOH B 25 525 75 HOH HOH . 
F 3 HOH B 26 526 158 HOH HOH . 
F 3 HOH B 27 527 174 HOH HOH . 
F 3 HOH B 28 528 86 HOH HOH . 
F 3 HOH B 29 529 54 HOH HOH . 
F 3 HOH B 30 530 74 HOH HOH . 
F 3 HOH B 31 531 60 HOH HOH . 
F 3 HOH B 32 532 14 HOH HOH . 
F 3 HOH B 33 533 149 HOH HOH . 
F 3 HOH B 34 534 69 HOH HOH . 
F 3 HOH B 35 535 73 HOH HOH . 
F 3 HOH B 36 536 123 HOH HOH . 
F 3 HOH B 37 537 33 HOH HOH . 
F 3 HOH B 38 538 52 HOH HOH . 
F 3 HOH B 39 539 146 HOH HOH . 
F 3 HOH B 40 540 112 HOH HOH . 
F 3 HOH B 41 541 32 HOH HOH . 
F 3 HOH B 42 542 157 HOH HOH . 
F 3 HOH B 43 543 83 HOH HOH . 
F 3 HOH B 44 544 166 HOH HOH . 
F 3 HOH B 45 545 162 HOH HOH . 
F 3 HOH B 46 546 28 HOH HOH . 
F 3 HOH B 47 547 51 HOH HOH . 
F 3 HOH B 48 548 19 HOH HOH . 
F 3 HOH B 49 549 144 HOH HOH . 
F 3 HOH B 50 550 77 HOH HOH . 
F 3 HOH B 51 551 106 HOH HOH . 
F 3 HOH B 52 552 165 HOH HOH . 
F 3 HOH B 53 553 117 HOH HOH . 
F 3 HOH B 54 554 156 HOH HOH . 
F 3 HOH B 55 555 173 HOH HOH . 
F 3 HOH B 56 556 88 HOH HOH . 
F 3 HOH B 57 557 120 HOH HOH . 
F 3 HOH B 58 558 46 HOH HOH . 
F 3 HOH B 59 559 114 HOH HOH . 
F 3 HOH B 60 560 34 HOH HOH . 
F 3 HOH B 61 561 171 HOH HOH . 
F 3 HOH B 62 562 102 HOH HOH . 
F 3 HOH B 63 563 190 HOH HOH . 
F 3 HOH B 64 564 63 HOH HOH . 
F 3 HOH B 65 565 108 HOH HOH . 
F 3 HOH B 66 566 104 HOH HOH . 
F 3 HOH B 67 567 145 HOH HOH . 
F 3 HOH B 68 568 178 HOH HOH . 
F 3 HOH B 69 569 189 HOH HOH . 
F 3 HOH B 70 570 151 HOH HOH . 
F 3 HOH B 71 571 124 HOH HOH . 
F 3 HOH B 72 572 187 HOH HOH . 
F 3 HOH B 73 573 180 HOH HOH . 
F 3 HOH B 74 574 35 HOH HOH . 
F 3 HOH B 75 575 53 HOH HOH . 
F 3 HOH B 76 576 153 HOH HOH . 
F 3 HOH B 77 577 136 HOH HOH . 
F 3 HOH B 78 578 115 HOH HOH . 
F 3 HOH B 79 579 118 HOH HOH . 
F 3 HOH B 80 580 195 HOH HOH . 
F 3 HOH B 81 581 160 HOH HOH . 
F 3 HOH B 82 582 70 HOH HOH . 
F 3 HOH B 83 583 81 HOH HOH . 
F 3 HOH B 84 584 168 HOH HOH . 
F 3 HOH B 85 585 176 HOH HOH . 
F 3 HOH B 86 586 161 HOH HOH . 
F 3 HOH B 87 587 181 HOH HOH . 
F 3 HOH B 88 588 167 HOH HOH . 
F 3 HOH B 89 589 95 HOH HOH . 
F 3 HOH B 90 590 134 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 O OP3 5HM . . . D 2 10.774 56.71 131.256 1 17.68 ? OP3 5HM 401 B 1 
HETATM 2 P P 5HM . . . D 2 9.864 55.589 131.598 1 18.21 ? P 5HM 401 B 1 
HETATM 3 O OP1 5HM . . . D 2 8.721 55.378 130.496 1 17.52 ? OP1 5HM 401 B 1 
HETATM 4 O OP2 5HM . . . D 2 9.192 55.815 133.038 1 17.78 ? OP2 5HM 401 B 1 
HETATM 5 O O5' 5HM . . . D 2 10.782 54.278 131.676 1 18.2 ? O5' 5HM 401 B 1 
HETATM 6 C C5' 5HM . . . D 2 10.221 53.013 131.987 1 18.77 ? C5' 5HM 401 B 1 
HETATM 7 C C4' 5HM . . . D 2 10.316 52.145 130.744 1 18.92 ? C4' 5HM 401 B 1 
HETATM 8 O O4' 5HM . . . D 2 10.417 50.771 131.108 1 19.22 ? O4' 5HM 401 B 1 
HETATM 9 C C3' 5HM . . . D 2 9.11 52.232 129.83 1 19.15 ? C3' 5HM 401 B 1 
HETATM 10 O O3' 5HM . . . D 2 9.19 53.345 128.932 1 18.98 ? O3' 5HM 401 B 1 
HETATM 11 C C2' 5HM . . . D 2 9.146 50.884 129.145 1 19.46 ? C2' 5HM 401 B 1 
HETATM 12 O O2' 5HM . . . D 2 10.086 50.875 128.075 1 19.59 ? O2' 5HM 401 B 1 
HETATM 13 C C1' 5HM . . . D 2 9.723 49.936 130.18 1 19.71 ? C1' 5HM 401 B 1 
HETATM 14 N N1 5HM . . . D 2 8.749 49.088 130.882 1 20.33 ? N1 5HM 401 B 1 
HETATM 15 C C2 5HM . . . D 2 7.839 48.272 130.155 1 20.45 ? C2 5HM 401 B 1 
HETATM 16 O O2 5HM . . . D 2 7.818 48.303 128.899 1 19.01 ? O2 5HM 401 B 1 
HETATM 17 C C6 5HM . . . D 2 8.793 49.026 132.232 1 21.13 ? C6 5HM 401 B 1 
HETATM 18 C C5 5HM . . . D 2 7.915 48.207 132.931 1 22.03 ? C5 5HM 401 B 1 
HETATM 19 C CM5 5HM . . . D 2 8.003 48.191 134.44 1 22.94 ? CM5 5HM 401 B 1 
HETATM 20 O OM5 5HM . . . D 2 9.078 47.312 134.779 1 24.76 ? OM5 5HM 401 B 1 
HETATM 21 C C4 5HM . . . D 2 6.95 47.376 132.157 1 22 ? C4 5HM 401 B 1 
HETATM 22 N N3 5HM . . . D 2 6.971 47.462 130.804 1 20.5 ? N3 5HM 401 B 1 
HETATM 23 N N4 5HM . . . D 2 6.056 46.547 132.754 1 22 ? N4 5HM 401 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           23 
#