data_5ZDN
#
_model_server_result.job_id            OUnnqS-zyquIQCFdBtCwiQ 
_model_server_result.datetime_utc      '2024-11-30 21:07:13' 
_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          5zdn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    5ZDN 
#
_exptl.entry_id    5ZDN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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            5ZDN 
_cell.length_a            56.165 
_cell.length_b            77.452 
_cell.length_c            96.566 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZDN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 56.165 0 48.283 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 ASN 113 A ASN 109 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
metalc ? metalc2 A OD2 ASP 129 A ASP 125 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc3 A O GLU 131 A GLU 127 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc4 A OE1 GLU 131 A GLU 127 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? 
metalc ? metalc5 A OD2 ASP 133 A ASP 129 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc6 A OD1 ASP 133 A ASP 129 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc7 A OD2 ASP 147 A ASP 143 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc8 B O3B CDP . A CDP 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc9 B O2A CDP . A CDP 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc10 B O1B CDP . A CDP 301 1_555 F MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc11 B O1B CDP . A CDP 301 1_555 F MG MG . A MG 305 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc12 C MG MG . A MG 302 1_555 H O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc13 D MG MG . A MG 303 1_555 H O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc14 D MG MG . A MG 303 1_555 H O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc15 D MG MG . A MG 303 1_555 H O HOH . A HOH 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc16 E MG MG . A MG 304 1_555 H O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
metalc ? metalc17 E MG MG . A MG 304 1_555 H O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? 
metalc ? metalc18 E MG MG . A MG 304 1_555 H O HOH . A HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc19 E MG MG . A MG 304 1_555 H O HOH . A HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc20 F MG MG . A MG 305 1_555 H O HOH . A HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc21 F MG MG . A MG 305 1_555 H O HOH . A HOH 419 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc22 F MG MG . A MG 305 1_555 H O HOH . A HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc23 F MG MG . A MG 305 1_555 H O HOH . A HOH 426 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc24 F MG MG . A MG 305 1_555 H O HOH . A HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? 
metalc ? metalc25 F MG MG . A MG 305 1_555 H O HOH . A HOH 441 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? 
#
_chem_comp.formula           'C9 H15 N3 O11 P2' 
_chem_comp.formula_weight    403.176 
_chem_comp.id                CDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-DIPHOSPHATE" 
_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
O3B PB CDP sing 70 n n 
PB O1B CDP doub 71 n n 
PB O2B CDP sing 72 n n 
PB O3A CDP sing 73 n n 
O3A PA CDP sing 74 n n 
PA O1A CDP doub 75 n n 
PA O2A CDP sing 76 n n 
PA O5' CDP sing 77 n n 
O5' C5' CDP sing 78 n n 
C5' C4' CDP sing 79 n n 
C5' "H5'1" CDP sing 80 n n 
C5' "H5'2" CDP sing 81 n n 
C4' O4' CDP sing 82 n n 
C4' C3' CDP sing 83 n n 
C4' H4' CDP sing 84 n n 
O4' C1' CDP sing 85 n n 
C3' O3' CDP sing 86 n n 
C3' C2' CDP sing 87 n n 
C3' H3' CDP sing 88 n n 
O3' HA CDP sing 89 n n 
C2' O2' CDP sing 90 n n 
C2' C1' CDP sing 91 n n 
C2' H2' CDP sing 92 n n 
O2' HB CDP sing 93 n n 
C1' N1 CDP sing 94 n n 
C1' H1' CDP sing 95 n n 
N1 C2 CDP sing 96 n n 
N1 C6 CDP sing 97 n n 
C2 O2 CDP doub 98 n n 
C2 N3 CDP sing 99 n n 
N3 C4 CDP doub 100 n n 
C4 N4 CDP sing 101 n n 
C4 C5 CDP sing 102 n n 
N4 H4N1 CDP sing 103 n n 
N4 H4N2 CDP sing 104 n n 
C5 C6 CDP doub 105 n n 
C5 H5 CDP sing 106 n n 
C6 H6 CDP sing 107 n n 
HO1 O2A CDP sing 108 n n 
HO2 O2B CDP sing 109 n n 
HO3 O3B CDP sing 110 n n 
#
_atom_sites.entry_id                     5ZDN 
_atom_sites.fract_transf_matrix[1][1]    0.017805 
_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]    0.012911 
_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]    0.010356 
_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 CDP A 1 301 301 CDP CDP . 
C 3 MG A 1 302 302 MG MG . 
D 3 MG A 1 303 303 MG MG . 
E 3 MG A 1 304 304 MG MG . 
F 3 MG A 1 305 305 MG MG . 
G 4 GOL A 1 306 306 GOL GOL . 
H 5 HOH A 1 401 56 HOH HOH . 
H 5 HOH A 2 402 41 HOH HOH . 
H 5 HOH A 3 403 52 HOH HOH . 
H 5 HOH A 4 404 40 HOH HOH . 
H 5 HOH A 5 405 4 HOH HOH . 
H 5 HOH A 6 406 38 HOH HOH . 
H 5 HOH A 7 407 26 HOH HOH . 
H 5 HOH A 8 408 21 HOH HOH . 
H 5 HOH A 9 409 65 HOH HOH . 
H 5 HOH A 10 410 11 HOH HOH . 
H 5 HOH A 11 411 34 HOH HOH . 
H 5 HOH A 12 412 59 HOH HOH . 
H 5 HOH A 13 413 13 HOH HOH . 
H 5 HOH A 14 414 8 HOH HOH . 
H 5 HOH A 15 415 22 HOH HOH . 
H 5 HOH A 16 416 48 HOH HOH . 
H 5 HOH A 17 417 16 HOH HOH . 
H 5 HOH A 18 418 5 HOH HOH . 
H 5 HOH A 19 419 68 HOH HOH . 
H 5 HOH A 20 420 19 HOH HOH . 
H 5 HOH A 21 421 63 HOH HOH . 
H 5 HOH A 22 422 33 HOH HOH . 
H 5 HOH A 23 423 17 HOH HOH . 
H 5 HOH A 24 424 32 HOH HOH . 
H 5 HOH A 25 425 18 HOH HOH . 
H 5 HOH A 26 426 70 HOH HOH . 
H 5 HOH A 27 427 64 HOH HOH . 
H 5 HOH A 28 428 1 HOH HOH . 
H 5 HOH A 29 429 53 HOH HOH . 
H 5 HOH A 30 430 50 HOH HOH . 
H 5 HOH A 31 431 45 HOH HOH . 
H 5 HOH A 32 432 72 HOH HOH . 
H 5 HOH A 33 433 29 HOH HOH . 
H 5 HOH A 34 434 24 HOH HOH . 
H 5 HOH A 35 435 30 HOH HOH . 
H 5 HOH A 36 436 12 HOH HOH . 
H 5 HOH A 37 437 15 HOH HOH . 
H 5 HOH A 38 438 62 HOH HOH . 
H 5 HOH A 39 439 71 HOH HOH . 
H 5 HOH A 40 440 6 HOH HOH . 
H 5 HOH A 41 441 69 HOH HOH . 
H 5 HOH A 42 442 47 HOH HOH . 
H 5 HOH A 43 443 49 HOH HOH . 
H 5 HOH A 44 444 60 HOH HOH . 
H 5 HOH A 45 445 57 HOH HOH . 
H 5 HOH A 46 446 31 HOH HOH . 
H 5 HOH A 47 447 7 HOH HOH . 
H 5 HOH A 48 448 42 HOH HOH . 
H 5 HOH A 49 449 10 HOH HOH . 
H 5 HOH A 50 450 61 HOH HOH . 
H 5 HOH A 51 451 25 HOH HOH . 
H 5 HOH A 52 452 9 HOH HOH . 
H 5 HOH A 53 453 35 HOH HOH . 
H 5 HOH A 54 454 28 HOH HOH . 
H 5 HOH A 55 455 2 HOH HOH . 
H 5 HOH A 56 456 73 HOH HOH . 
H 5 HOH A 57 457 43 HOH HOH . 
H 5 HOH A 58 458 27 HOH HOH . 
H 5 HOH A 59 459 3 HOH HOH . 
H 5 HOH A 60 460 54 HOH HOH . 
H 5 HOH A 61 461 14 HOH HOH . 
H 5 HOH A 62 462 23 HOH HOH . 
H 5 HOH A 63 463 67 HOH HOH . 
H 5 HOH A 64 464 44 HOH HOH . 
H 5 HOH A 65 465 20 HOH HOH . 
H 5 HOH A 66 466 66 HOH HOH . 
H 5 HOH A 67 467 51 HOH HOH . 
H 5 HOH A 68 468 46 HOH HOH . 
H 5 HOH A 69 469 36 HOH HOH . 
H 5 HOH A 70 470 58 HOH HOH . 
H 5 HOH A 71 471 37 HOH HOH . 
H 5 HOH A 72 472 55 HOH HOH . 
H 5 HOH A 73 473 39 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 O3B CDP . . . B 2 25.857 14.139 27.246 1 20.37 ? O3B CDP 301 A 1 
HETATM 2 P PB CDP . . . B 2 27.441 14.43 27.477 1 22.38 ? PB CDP 301 A 1 
HETATM 3 O O1B CDP . . . B 2 28.025 14.332 26.148 1 23.24 ? O1B CDP 301 A 1 
HETATM 4 O O2B CDP . . . B 2 27.712 15.633 28.245 1 23.91 ? O2B CDP 301 A 1 
HETATM 5 O O3A CDP . . . B 2 28.049 13.237 28.334 1 24.17 ? O3A CDP 301 A 1 
HETATM 6 P PA CDP . . . B 2 27.595 11.928 29.134 1 28.84 ? PA CDP 301 A 1 
HETATM 7 O O1A CDP . . . B 2 28.126 10.673 28.544 1 28.32 ? O1A CDP 301 A 1 
HETATM 8 O O2A CDP . . . B 2 26.068 12.026 29.231 1 23.96 ? O2A CDP 301 A 1 
HETATM 9 O O5' CDP . . . B 2 28.07 12.097 30.675 1 25.42 ? O5' CDP 301 A 1 
HETATM 10 C C5' CDP . . . B 2 27.758 13.352 31.157 1 26.16 ? C5' CDP 301 A 1 
HETATM 11 C C4' CDP . . . B 2 28.017 13.485 32.603 1 26.65 ? C4' CDP 301 A 1 
HETATM 12 O O4' CDP . . . B 2 27.212 12.615 33.406 1 23.23 ? O4' CDP 301 A 1 
HETATM 13 C C3' CDP . . . B 2 29.453 13.127 32.976 1 25.74 ? C3' CDP 301 A 1 
HETATM 14 O O3' CDP . . . B 2 30.368 14.147 32.617 1 28.46 ? O3' CDP 301 A 1 
HETATM 15 C C2' CDP . . . B 2 29.268 12.906 34.466 1 24.82 ? C2' CDP 301 A 1 
HETATM 16 O O2' CDP . . . B 2 29.151 14.221 35.044 1 25.05 ? O2' CDP 301 A 1 
HETATM 17 C C1' CDP . . . B 2 27.868 12.241 34.595 1 24.24 ? C1' CDP 301 A 1 
HETATM 18 N N1 CDP . . . B 2 27.911 10.769 34.691 1 23.09 ? N1 CDP 301 A 1 
HETATM 19 C C2 CDP . . . B 2 28.353 10.205 35.901 1 25.07 ? C2 CDP 301 A 1 
HETATM 20 O O2 CDP . . . B 2 28.648 10.974 36.813 1 29.51 ? O2 CDP 301 A 1 
HETATM 21 N N3 CDP . . . B 2 28.486 8.894 36.054 1 25.25 ? N3 CDP 301 A 1 
HETATM 22 C C4 CDP . . . B 2 28.173 8.145 34.975 1 23.55 ? C4 CDP 301 A 1 
HETATM 23 N N4 CDP . . . B 2 28.266 6.837 35.003 1 23.31 ? N4 CDP 301 A 1 
HETATM 24 C C5 CDP . . . B 2 27.827 8.701 33.782 1 22.82 ? C5 CDP 301 A 1 
HETATM 25 C C6 CDP . . . B 2 27.677 10.027 33.639 1 21.73 ? C6 CDP 301 A 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           60 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           624 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#