data_2ATV
#
_model_server_result.job_id            -PF1vrc4rkVVTAZ08nKLnw 
_model_server_result.datetime_utc      '2025-02-26 21:39:29' 
_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          2atv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":415}' 
#
_entry.id    2ATV 
#
_exptl.entry_id    2ATV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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         90 
_cell.entry_id            2ATV 
_cell.length_a            76.405 
_cell.length_b            76.405 
_cell.length_c            107.876 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ATV 
_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 
_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                             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 OG SER 42 A SER 20 1_555 B MG MG . A MG 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc2 B MG MG . A MG 175 1_555 C O3B GDP . A GDP 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc3 B MG MG . A MG 175 1_555 D O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc4 B MG MG . A MG 175 1_555 D O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc5 B MG MG . A MG 175 1_555 D O HOH . A HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc6 B MG MG . A MG 175 1_555 D O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
#
_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                     2ATV 
_atom_sites.fract_transf_matrix[1][1]    0.013088 
_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]    0.013088 
_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]    0.00927 
_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 MG A 1 175 1 MG MG . 
C 3 GDP A 1 415 415 GDP GDP . 
D 4 HOH A 1 416 3 HOH HOH . 
D 4 HOH A 2 417 5 HOH HOH . 
D 4 HOH A 3 418 6 HOH HOH . 
D 4 HOH A 4 419 9 HOH HOH . 
D 4 HOH A 5 420 10 HOH HOH . 
D 4 HOH A 6 421 11 HOH HOH . 
D 4 HOH A 7 422 12 HOH HOH . 
D 4 HOH A 8 423 13 HOH HOH . 
D 4 HOH A 9 424 16 HOH HOH . 
D 4 HOH A 10 425 17 HOH HOH . 
D 4 HOH A 11 426 18 HOH HOH . 
D 4 HOH A 12 427 19 HOH HOH . 
D 4 HOH A 13 428 20 HOH HOH . 
D 4 HOH A 14 429 22 HOH HOH . 
D 4 HOH A 15 430 23 HOH HOH . 
D 4 HOH A 16 431 24 HOH HOH . 
D 4 HOH A 17 432 25 HOH HOH . 
D 4 HOH A 18 433 26 HOH HOH . 
D 4 HOH A 19 434 27 HOH HOH . 
D 4 HOH A 20 435 28 HOH HOH . 
D 4 HOH A 21 436 29 HOH HOH . 
D 4 HOH A 22 437 30 HOH HOH . 
D 4 HOH A 23 438 31 HOH HOH . 
D 4 HOH A 24 439 33 HOH HOH . 
D 4 HOH A 25 440 34 HOH HOH . 
D 4 HOH A 26 441 36 HOH HOH . 
D 4 HOH A 27 442 37 HOH HOH . 
D 4 HOH A 28 443 38 HOH HOH . 
D 4 HOH A 29 444 39 HOH HOH . 
D 4 HOH A 30 445 40 HOH HOH . 
D 4 HOH A 31 446 41 HOH HOH . 
D 4 HOH A 32 447 42 HOH HOH . 
D 4 HOH A 33 448 44 HOH HOH . 
D 4 HOH A 34 449 45 HOH HOH . 
D 4 HOH A 35 450 46 HOH HOH . 
D 4 HOH A 36 451 47 HOH HOH . 
D 4 HOH A 37 452 48 HOH HOH . 
D 4 HOH A 38 453 49 HOH HOH . 
D 4 HOH A 39 454 50 HOH HOH . 
D 4 HOH A 40 455 51 HOH HOH . 
D 4 HOH A 41 456 52 HOH HOH . 
D 4 HOH A 42 457 54 HOH HOH . 
D 4 HOH A 43 458 56 HOH HOH . 
D 4 HOH A 44 459 58 HOH HOH . 
D 4 HOH A 45 460 59 HOH HOH . 
D 4 HOH A 46 461 60 HOH HOH . 
D 4 HOH A 47 462 61 HOH HOH . 
D 4 HOH A 48 463 62 HOH HOH . 
D 4 HOH A 49 464 64 HOH HOH . 
D 4 HOH A 50 465 65 HOH HOH . 
D 4 HOH A 51 466 66 HOH HOH . 
D 4 HOH A 52 467 67 HOH HOH . 
D 4 HOH A 53 468 69 HOH HOH . 
D 4 HOH A 54 469 70 HOH HOH . 
D 4 HOH A 55 470 73 HOH HOH . 
D 4 HOH A 56 471 76 HOH HOH . 
D 4 HOH A 57 472 77 HOH HOH . 
D 4 HOH A 58 473 78 HOH HOH . 
D 4 HOH A 59 474 79 HOH HOH . 
D 4 HOH A 60 475 80 HOH HOH . 
D 4 HOH A 61 476 82 HOH HOH . 
D 4 HOH A 62 477 85 HOH HOH . 
D 4 HOH A 63 478 86 HOH HOH . 
D 4 HOH A 64 479 88 HOH HOH . 
D 4 HOH A 65 480 89 HOH HOH . 
D 4 HOH A 66 481 94 HOH HOH . 
D 4 HOH A 67 482 95 HOH HOH . 
D 4 HOH A 68 483 98 HOH HOH . 
D 4 HOH A 69 484 99 HOH HOH . 
D 4 HOH A 70 485 102 HOH HOH . 
D 4 HOH A 71 486 103 HOH HOH . 
D 4 HOH A 72 487 106 HOH HOH . 
D 4 HOH A 73 488 108 HOH HOH . 
D 4 HOH A 74 489 109 HOH HOH . 
D 4 HOH A 75 490 110 HOH HOH . 
D 4 HOH A 76 491 111 HOH HOH . 
D 4 HOH A 77 492 112 HOH HOH . 
D 4 HOH A 78 493 116 HOH HOH . 
D 4 HOH A 79 494 117 HOH HOH . 
D 4 HOH A 80 495 130 HOH HOH . 
D 4 HOH A 81 496 132 HOH HOH . 
D 4 HOH A 82 497 134 HOH HOH . 
D 4 HOH A 83 498 136 HOH HOH . 
D 4 HOH A 84 499 137 HOH HOH . 
D 4 HOH A 85 500 138 HOH HOH . 
D 4 HOH A 86 501 139 HOH HOH . 
D 4 HOH A 87 502 140 HOH HOH . 
D 4 HOH A 88 503 141 HOH HOH . 
D 4 HOH A 89 504 142 HOH HOH . 
D 4 HOH A 90 505 143 HOH HOH . 
D 4 HOH A 91 506 144 HOH HOH . 
D 4 HOH A 92 507 145 HOH HOH . 
D 4 HOH A 93 508 146 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 . . . C 3 12.566 20.692 9.643 1 27.86 ? PB GDP 415 A 1 
HETATM 2 O O1B GDP . . . C 3 13.121 19.695 10.635 1 30.84 ? O1B GDP 415 A 1 
HETATM 3 O O2B GDP . . . C 3 12.288 22.026 10.323 1 28.73 ? O2B GDP 415 A 1 
HETATM 4 O O3B GDP . . . C 3 13.468 20.878 8.449 1 25.56 ? O3B GDP 415 A 1 
HETATM 5 O O3A GDP . . . C 3 11.131 20.15 9.194 1 29.41 ? O3A GDP 415 A 1 
HETATM 6 P PA GDP . . . C 3 10.737 19.265 7.907 1 29.66 ? PA GDP 415 A 1 
HETATM 7 O O1A GDP . . . C 3 10.739 20.083 6.646 1 29.01 ? O1A GDP 415 A 1 
HETATM 8 O O2A GDP . . . C 3 11.645 18.058 7.829 1 32.47 ? O2A GDP 415 A 1 
HETATM 9 O O5' GDP . . . C 3 9.233 18.906 8.22 1 29.38 ? O5' GDP 415 A 1 
HETATM 10 C C5' GDP . . . C 3 9.024 18.073 9.364 1 31.5 ? C5' GDP 415 A 1 
HETATM 11 C C4' GDP . . . C 3 7.767 17.276 9.171 1 29.83 ? C4' GDP 415 A 1 
HETATM 12 O O4' GDP . . . C 3 6.637 18.157 9.087 1 34.08 ? O4' GDP 415 A 1 
HETATM 13 C C3' GDP . . . C 3 7.756 16.466 7.891 1 34.31 ? C3' GDP 415 A 1 
HETATM 14 O O3' GDP . . . C 3 7.053 15.264 8.189 1 35.42 ? O3' GDP 415 A 1 
HETATM 15 C C2' GDP . . . C 3 6.954 17.301 6.916 1 29.83 ? C2' GDP 415 A 1 
HETATM 16 O O2' GDP . . . C 3 6.231 16.563 5.935 1 35.29 ? O2' GDP 415 A 1 
HETATM 17 C C1' GDP . . . C 3 5.975 17.985 7.835 1 29.58 ? C1' GDP 415 A 1 
HETATM 18 N N9 GDP . . . C 3 5.545 19.322 7.357 1 29.94 ? N9 GDP 415 A 1 
HETATM 19 C C8 GDP . . . C 3 6.338 20.341 6.984 1 25.98 ? C8 GDP 415 A 1 
HETATM 20 N N7 GDP . . . C 3 5.607 21.418 6.634 1 28.37 ? N7 GDP 415 A 1 
HETATM 21 C C5 GDP . . . C 3 4.314 21.078 6.799 1 22.82 ? C5 GDP 415 A 1 
HETATM 22 C C6 GDP . . . C 3 3.019 21.722 6.64 1 32.74 ? C6 GDP 415 A 1 
HETATM 23 O O6 GDP . . . C 3 2.937 22.892 6.238 1 30.59 ? O6 GDP 415 A 1 
HETATM 24 N N1 GDP . . . C 3 1.922 21.013 6.944 1 31.6 ? N1 GDP 415 A 1 
HETATM 25 C C2 GDP . . . C 3 1.959 19.736 7.369 1 34.61 ? C2 GDP 415 A 1 
HETATM 26 N N2 GDP . . . C 3 0.799 19.112 7.636 1 33.04 ? N2 GDP 415 A 1 
HETATM 27 N N3 GDP . . . C 3 3.104 19.068 7.543 1 29.64 ? N3 GDP 415 A 1 
HETATM 28 C C4 GDP . . . C 3 4.285 19.691 7.286 1 30.72 ? C4 GDP 415 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#