data_2CMK
#
_model_server_result.job_id            99kQL5rlHBiEqfHjTEqIOA 
_model_server_result.datetime_utc      '2025-01-02 23:41:14' 
_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          2cmk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":407}' 
#
_entry.id    2CMK 
#
_exptl.entry_id    2CMK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          3 
_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            2CMK 
_cell.length_a            77.268 
_cell.length_b            77.268 
_cell.length_c            81.232 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2CMK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     2CMK 
_atom_sites.fract_transf_matrix[1][1]    0.012942 
_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]    0.012942 
_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]    0.01231 
_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 SO4 A 1 228 1 SO4 SO4 . 
C 2 SO4 A 1 229 2 SO4 SO4 . 
D 3 CDP A 1 407 407 CDP CDP . 
E 4 HOH A 1 408 1 HOH HOH . 
E 4 HOH A 2 409 2 HOH HOH . 
E 4 HOH A 3 410 3 HOH HOH . 
E 4 HOH A 4 411 4 HOH HOH . 
E 4 HOH A 5 412 5 HOH HOH . 
E 4 HOH A 6 413 6 HOH HOH . 
E 4 HOH A 7 414 7 HOH HOH . 
E 4 HOH A 8 415 8 HOH HOH . 
E 4 HOH A 9 416 9 HOH HOH . 
E 4 HOH A 10 417 10 HOH HOH . 
E 4 HOH A 11 418 11 HOH HOH . 
E 4 HOH A 12 419 12 HOH HOH . 
E 4 HOH A 13 420 13 HOH HOH . 
E 4 HOH A 14 421 14 HOH HOH . 
E 4 HOH A 15 422 15 HOH HOH . 
E 4 HOH A 16 423 16 HOH HOH . 
E 4 HOH A 17 424 17 HOH HOH . 
E 4 HOH A 18 425 18 HOH HOH . 
E 4 HOH A 19 426 19 HOH HOH . 
E 4 HOH A 20 427 20 HOH HOH . 
E 4 HOH A 21 428 21 HOH HOH . 
E 4 HOH A 22 429 22 HOH HOH . 
E 4 HOH A 23 430 23 HOH HOH . 
E 4 HOH A 24 431 24 HOH HOH . 
E 4 HOH A 25 432 25 HOH HOH . 
E 4 HOH A 26 433 26 HOH HOH . 
E 4 HOH A 27 434 27 HOH HOH . 
E 4 HOH A 28 435 28 HOH HOH . 
E 4 HOH A 29 436 29 HOH HOH . 
E 4 HOH A 30 437 30 HOH HOH . 
E 4 HOH A 31 438 31 HOH HOH . 
E 4 HOH A 32 439 32 HOH HOH . 
E 4 HOH A 33 440 33 HOH HOH . 
E 4 HOH A 34 441 34 HOH HOH . 
E 4 HOH A 35 442 35 HOH HOH . 
E 4 HOH A 36 443 36 HOH HOH . 
E 4 HOH A 37 444 37 HOH HOH . 
E 4 HOH A 38 445 38 HOH HOH . 
E 4 HOH A 39 446 39 HOH HOH . 
E 4 HOH A 40 447 40 HOH HOH . 
E 4 HOH A 41 448 41 HOH HOH . 
E 4 HOH A 42 449 42 HOH HOH . 
E 4 HOH A 43 450 43 HOH HOH . 
E 4 HOH A 44 451 44 HOH HOH . 
E 4 HOH A 45 452 45 HOH HOH . 
E 4 HOH A 46 453 46 HOH HOH . 
E 4 HOH A 47 454 47 HOH HOH . 
E 4 HOH A 48 455 48 HOH HOH . 
E 4 HOH A 49 456 49 HOH HOH . 
E 4 HOH A 50 457 50 HOH HOH . 
E 4 HOH A 51 458 51 HOH HOH . 
E 4 HOH A 52 459 52 HOH HOH . 
E 4 HOH A 53 460 53 HOH HOH . 
E 4 HOH A 54 461 54 HOH HOH . 
E 4 HOH A 55 462 55 HOH HOH . 
E 4 HOH A 56 463 56 HOH HOH . 
E 4 HOH A 57 464 57 HOH HOH . 
E 4 HOH A 58 465 58 HOH HOH . 
E 4 HOH A 59 466 59 HOH HOH . 
E 4 HOH A 60 467 60 HOH HOH . 
E 4 HOH A 61 468 61 HOH HOH . 
E 4 HOH A 62 469 62 HOH HOH . 
E 4 HOH A 63 470 63 HOH HOH . 
E 4 HOH A 64 471 64 HOH HOH . 
E 4 HOH A 65 472 65 HOH HOH . 
E 4 HOH A 66 473 66 HOH HOH . 
E 4 HOH A 67 474 67 HOH HOH . 
E 4 HOH A 68 475 68 HOH HOH . 
E 4 HOH A 69 476 69 HOH HOH . 
E 4 HOH A 70 477 70 HOH HOH . 
E 4 HOH A 71 478 71 HOH HOH . 
E 4 HOH A 72 479 72 HOH HOH . 
E 4 HOH A 73 480 73 HOH HOH . 
E 4 HOH A 74 481 74 HOH HOH . 
E 4 HOH A 75 482 76 HOH HOH . 
E 4 HOH A 76 483 77 HOH HOH . 
E 4 HOH A 77 484 78 HOH HOH . 
E 4 HOH A 78 485 79 HOH HOH . 
E 4 HOH A 79 486 80 HOH HOH . 
E 4 HOH A 80 487 81 HOH HOH . 
E 4 HOH A 81 488 82 HOH HOH . 
E 4 HOH A 82 489 83 HOH HOH . 
E 4 HOH A 83 490 84 HOH HOH . 
E 4 HOH A 84 491 85 HOH HOH . 
E 4 HOH A 85 492 86 HOH HOH . 
E 4 HOH A 86 493 87 HOH HOH . 
E 4 HOH A 87 494 88 HOH HOH . 
E 4 HOH A 88 495 89 HOH HOH . 
E 4 HOH A 89 496 90 HOH HOH . 
E 4 HOH A 90 497 91 HOH HOH . 
E 4 HOH A 91 498 92 HOH HOH . 
E 4 HOH A 92 499 93 HOH HOH . 
E 4 HOH A 93 500 94 HOH HOH . 
E 4 HOH A 94 501 95 HOH HOH . 
E 4 HOH A 95 502 96 HOH HOH . 
E 4 HOH A 96 503 97 HOH HOH . 
E 4 HOH A 97 504 98 HOH HOH . 
E 4 HOH A 98 505 99 HOH HOH . 
E 4 HOH A 99 506 100 HOH HOH . 
E 4 HOH A 100 507 101 HOH HOH . 
E 4 HOH A 101 508 102 HOH HOH . 
E 4 HOH A 102 509 103 HOH HOH . 
E 4 HOH A 103 510 104 HOH HOH . 
E 4 HOH A 104 511 105 HOH HOH . 
E 4 HOH A 105 512 106 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 . . . D 3 63.223 54.724 25.016 1 83.88 ? O3B CDP 407 A 1 
HETATM 2 P PB CDP . . . D 3 61.765 54.98 25.781 1 79.64 ? PB CDP 407 A 1 
HETATM 3 O O1B CDP . . . D 3 60.679 54.061 25.072 1 79.17 ? O1B CDP 407 A 1 
HETATM 4 O O2B CDP . . . D 3 61.854 54.561 27.325 1 82.8 ? O2B CDP 407 A 1 
HETATM 5 O O3A CDP . . . D 3 61.36 56.645 25.696 1 41.41 ? O3A CDP 407 A 1 
HETATM 6 P PA CDP . . . D 3 61.118 57.441 24.232 1 29.19 ? PA CDP 407 A 1 
HETATM 7 O O1A CDP . . . D 3 62.151 56.978 23.191 1 31.5 ? O1A CDP 407 A 1 
HETATM 8 O O2A CDP . . . D 3 61.169 58.971 24.412 1 33.46 ? O2A CDP 407 A 1 
HETATM 9 O O5' CDP . . . D 3 59.628 57.162 23.608 1 37.76 ? O5' CDP 407 A 1 
HETATM 10 C C5' CDP . . . D 3 58.913 56.087 24.154 1 34.78 ? C5' CDP 407 A 1 
HETATM 11 C C4' CDP . . . D 3 57.901 55.526 23.243 1 32.65 ? C4' CDP 407 A 1 
HETATM 12 O O4' CDP . . . D 3 57.756 56.258 22.034 1 31.04 ? O4' CDP 407 A 1 
HETATM 13 C C3' CDP . . . D 3 58.664 54.253 22.852 1 32.54 ? C3' CDP 407 A 1 
HETATM 14 O O3' CDP . . . D 3 57.776 53.178 23.086 1 33.46 ? O3' CDP 407 A 1 
HETATM 15 C C2' CDP . . . D 3 58.985 54.42 21.395 1 32.05 ? C2' CDP 407 A 1 
HETATM 16 O O2' CDP . . . D 3 58.855 53.238 20.641 1 34.3 ? O2' CDP 407 A 1 
HETATM 17 C C1' CDP . . . D 3 57.965 55.418 20.927 1 30.87 ? C1' CDP 407 A 1 
HETATM 18 N N1 CDP . . . D 3 58.474 56.194 19.783 1 22.49 ? N1 CDP 407 A 1 
HETATM 19 C C2 CDP . . . D 3 58.158 55.884 18.472 1 25.64 ? C2 CDP 407 A 1 
HETATM 20 O O2 CDP . . . D 3 57.452 54.903 18.198 1 23.59 ? O2 CDP 407 A 1 
HETATM 21 N N3 CDP . . . D 3 58.576 56.616 17.413 1 20.52 ? N3 CDP 407 A 1 
HETATM 22 C C4 CDP . . . D 3 59.34 57.703 17.641 1 24.71 ? C4 CDP 407 A 1 
HETATM 23 N N4 CDP . . . D 3 59.757 58.431 16.603 1 17.94 ? N4 CDP 407 A 1 
HETATM 24 C C5 CDP . . . D 3 59.68 58.054 18.943 1 24.1 ? C5 CDP 407 A 1 
HETATM 25 C C6 CDP . . . D 3 59.224 57.266 19.967 1 19.93 ? C6 CDP 407 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           25 
#