data_3CPH
#
_model_server_result.job_id            KexGzidXhypqTXfS1wESkQ 
_model_server_result.datetime_utc      '2024-11-19 13:20:02' 
_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          3cph 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":302}' 
#
_entry.id    3CPH 
#
_exptl.entry_id    3CPH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-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         120 
_cell.entry_id            3CPH 
_cell.length_a            131.9 
_cell.length_b            131.9 
_cell.length_c            217.562 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CPH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_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,D,E,F,G 1 1 
C,H 2 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                      4 
_struct_asym.id                             E 
_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 B OG SER 34 A SER 34 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc2 D MG MG . A MG 301 1_555 E O2B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     3CPH 
_atom_sites.fract_transf_matrix[1][1]    0.007582 
_atom_sites.fract_transf_matrix[1][2]    0.004377 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008754 
_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]    0.004596 
_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
D 3 MG A 1 301 301 MG MG . 
E 4 GDP A 1 302 201 GDP GDP . 
F 5 HOH G 1 452 2 HOH HOH . 
F 5 HOH G 2 453 4 HOH HOH . 
F 5 HOH G 3 454 5 HOH HOH . 
F 5 HOH G 4 455 6 HOH HOH . 
F 5 HOH G 5 456 7 HOH HOH . 
F 5 HOH G 6 457 8 HOH HOH . 
F 5 HOH G 7 458 10 HOH HOH . 
F 5 HOH G 8 459 12 HOH HOH . 
F 5 HOH G 9 460 13 HOH HOH . 
F 5 HOH G 10 461 14 HOH HOH . 
F 5 HOH G 11 462 16 HOH HOH . 
F 5 HOH G 12 463 17 HOH HOH . 
F 5 HOH G 13 464 18 HOH HOH . 
F 5 HOH G 14 465 21 HOH HOH . 
F 5 HOH G 15 466 22 HOH HOH . 
F 5 HOH G 16 467 25 HOH HOH . 
F 5 HOH G 17 468 28 HOH HOH . 
F 5 HOH G 18 469 29 HOH HOH . 
F 5 HOH G 19 470 30 HOH HOH . 
F 5 HOH G 20 471 31 HOH HOH . 
F 5 HOH G 21 472 33 HOH HOH . 
F 5 HOH G 22 473 34 HOH HOH . 
F 5 HOH G 23 474 35 HOH HOH . 
F 5 HOH G 24 475 38 HOH HOH . 
F 5 HOH G 25 476 39 HOH HOH . 
F 5 HOH G 26 477 42 HOH HOH . 
F 5 HOH G 27 478 43 HOH HOH . 
F 5 HOH G 28 479 44 HOH HOH . 
F 5 HOH G 29 480 45 HOH HOH . 
F 5 HOH G 30 481 47 HOH HOH . 
F 5 HOH G 31 482 49 HOH HOH . 
F 5 HOH G 32 483 50 HOH HOH . 
F 5 HOH G 33 484 51 HOH HOH . 
F 5 HOH G 34 485 52 HOH HOH . 
F 5 HOH G 35 486 53 HOH HOH . 
F 5 HOH G 36 487 54 HOH HOH . 
F 5 HOH G 37 488 55 HOH HOH . 
F 5 HOH G 38 489 56 HOH HOH . 
F 5 HOH G 39 490 57 HOH HOH . 
F 5 HOH G 40 491 63 HOH HOH . 
F 5 HOH G 41 492 65 HOH HOH . 
F 5 HOH G 42 493 70 HOH HOH . 
F 5 HOH G 43 494 71 HOH HOH . 
F 5 HOH G 44 495 72 HOH HOH . 
F 5 HOH G 45 496 73 HOH HOH . 
F 5 HOH G 46 497 84 HOH HOH . 
F 5 HOH G 47 498 86 HOH HOH . 
G 5 HOH A 1 303 1 HOH HOH . 
G 5 HOH A 2 304 3 HOH HOH . 
G 5 HOH A 3 305 9 HOH HOH . 
G 5 HOH A 4 306 11 HOH HOH . 
G 5 HOH A 5 307 15 HOH HOH . 
G 5 HOH A 6 308 19 HOH HOH . 
G 5 HOH A 7 309 20 HOH HOH . 
G 5 HOH A 8 310 23 HOH HOH . 
G 5 HOH A 9 311 24 HOH HOH . 
G 5 HOH A 10 312 26 HOH HOH . 
G 5 HOH A 11 313 27 HOH HOH . 
G 5 HOH A 12 314 32 HOH HOH . 
G 5 HOH A 13 315 36 HOH HOH . 
G 5 HOH A 14 316 37 HOH HOH . 
G 5 HOH A 15 317 40 HOH HOH . 
G 5 HOH A 16 318 41 HOH HOH . 
G 5 HOH A 17 319 48 HOH HOH . 
G 5 HOH A 18 320 58 HOH HOH . 
G 5 HOH A 19 321 59 HOH HOH . 
G 5 HOH A 20 322 60 HOH HOH . 
G 5 HOH A 21 323 61 HOH HOH . 
G 5 HOH A 22 324 62 HOH HOH . 
G 5 HOH A 23 325 64 HOH HOH . 
G 5 HOH A 24 326 66 HOH HOH . 
G 5 HOH A 25 327 67 HOH HOH . 
G 5 HOH A 26 328 68 HOH HOH . 
G 5 HOH A 27 329 69 HOH HOH . 
G 5 HOH A 28 330 74 HOH HOH . 
G 5 HOH A 29 460 83 HOH HOH . 
H 5 HOH H 1 452 75 HOH HOH . 
H 5 HOH H 2 453 76 HOH HOH . 
H 5 HOH H 3 454 77 HOH HOH . 
H 5 HOH H 4 455 78 HOH HOH . 
H 5 HOH H 5 456 79 HOH HOH . 
H 5 HOH H 6 457 80 HOH HOH . 
H 5 HOH H 7 458 81 HOH HOH . 
H 5 HOH H 8 459 82 HOH HOH . 
H 5 HOH H 9 462 85 HOH HOH . 
H 5 HOH H 10 463 87 HOH HOH . 
H 5 HOH H 11 464 88 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 P PB GDP . . . E 4 55.824 19.15 8.269 1 41.18 ? PB GDP 302 A 1 
HETATM 2 O O1B GDP . . . E 4 55.245 19.777 9.506 1 41.56 ? O1B GDP 302 A 1 
HETATM 3 O O2B GDP . . . E 4 56.846 18.081 8.6 1 40.04 ? O2B GDP 302 A 1 
HETATM 4 O O3B GDP . . . E 4 54.637 18.592 7.516 1 40.03 ? O3B GDP 302 A 1 
HETATM 5 O O3A GDP . . . E 4 56.528 20.346 7.456 1 42.25 ? O3A GDP 302 A 1 
HETATM 6 P PA GDP . . . E 4 58.027 20.228 6.887 1 43.85 ? PA GDP 302 A 1 
HETATM 7 O O1A GDP . . . E 4 59.059 20.273 7.989 1 43.47 ? O1A GDP 302 A 1 
HETATM 8 O O2A GDP . . . E 4 58.149 18.94 6.1 1 44.81 ? O2A GDP 302 A 1 
HETATM 9 O O5' GDP . . . E 4 58.197 21.537 5.956 1 44.58 ? O5' GDP 302 A 1 
HETATM 10 C C5' GDP . . . E 4 57.057 22.224 5.415 1 46 ? C5' GDP 302 A 1 
HETATM 11 C C4' GDP . . . E 4 57.401 23.357 4.434 1 46.36 ? C4' GDP 302 A 1 
HETATM 12 O O4' GDP . . . E 4 57.428 24.63 5.104 1 47.22 ? O4' GDP 302 A 1 
HETATM 13 C C3' GDP . . . E 4 58.755 23.194 3.762 1 46.57 ? C3' GDP 302 A 1 
HETATM 14 O O3' GDP . . . E 4 58.683 23.631 2.41 1 46.71 ? O3' GDP 302 A 1 
HETATM 15 C C2' GDP . . . E 4 59.671 24.095 4.547 1 47.05 ? C2' GDP 302 A 1 
HETATM 16 O O2' GDP . . . E 4 60.731 24.623 3.745 1 47.62 ? O2' GDP 302 A 1 
HETATM 17 C C1' GDP . . . E 4 58.745 25.18 5.08 1 47.21 ? C1' GDP 302 A 1 
HETATM 18 N N9 GDP . . . E 4 59.159 25.575 6.438 1 47.12 ? N9 GDP 302 A 1 
HETATM 19 C C8 GDP . . . E 4 59.349 24.778 7.505 1 47.42 ? C8 GDP 302 A 1 
HETATM 20 N N7 GDP . . . E 4 59.741 25.501 8.591 1 47.39 ? N7 GDP 302 A 1 
HETATM 21 C C5 GDP . . . E 4 59.807 26.785 8.215 1 47.23 ? C5 GDP 302 A 1 
HETATM 22 C C6 GDP . . . E 4 60.152 28.08 8.849 1 47.02 ? C6 GDP 302 A 1 
HETATM 23 O O6 GDP . . . E 4 60.49 28.195 10.049 1 47.03 ? O6 GDP 302 A 1 
HETATM 24 N N1 GDP . . . E 4 60.081 29.161 8.072 1 47.52 ? N1 GDP 302 A 1 
HETATM 25 C C2 GDP . . . E 4 59.718 29.115 6.768 1 47.52 ? C2 GDP 302 A 1 
HETATM 26 N N2 GDP . . . E 4 59.668 30.267 6.05 1 47.51 ? N2 GDP 302 A 1 
HETATM 27 N N3 GDP . . . E 4 59.393 27.966 6.13 1 47.12 ? N3 GDP 302 A 1 
HETATM 28 C C4 GDP . . . E 4 59.424 26.808 6.793 1 47.07 ? C4 GDP 302 A 1 
#
_model_server_stats.io_time_ms              124 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           394 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#