data_3AB3
#
_model_server_result.job_id            8_i74aZYC8FqGl-C-20MzA 
_model_server_result.datetime_utc      '2024-12-30 17:20:54' 
_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          3ab3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    3AB3 
#
_exptl.entry_id    3AB3 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         77.77 
_cell.angle_beta          84.45 
_cell.angle_gamma         80.11 
_cell.entry_id            3AB3 
_cell.length_a            50.481 
_cell.length_b            70.64 
_cell.length_c            88.078 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AB3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 dimeric 2 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,E,F,G,K,L 1 1 
C,D,H,I,J,M,N 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 I N 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 47 A SER 62 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc2 A OG1 THR 188 A THR 203 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc3 F O3B GDP . A GDP 401 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc4 K O HOH . A HOH 408 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc5 K O HOH . A HOH 409 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? 
metalc ? metalc6 M O HOH . C HOH 1 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc7 C OG SER 47 C SER 62 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc8 C OG1 THR 188 C THR 203 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? 
metalc ? metalc9 M O HOH . C HOH 388 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc10 I O3B GDP . C GDP 402 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
#
_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 87 n n 
PB O2B GDP sing 88 n n 
PB O3B GDP sing 89 n n 
PB O3A GDP sing 90 n n 
O2B HOB2 GDP sing 91 n n 
O3B HOB3 GDP sing 92 n n 
O3A PA GDP sing 93 n n 
PA O1A GDP doub 94 n n 
PA O2A GDP sing 95 n n 
PA O5' GDP sing 96 n n 
O2A HOA2 GDP sing 97 n n 
O5' C5' GDP sing 98 n n 
C5' C4' GDP sing 99 n n 
C5' H5' GDP sing 100 n n 
C5' "H5''" GDP sing 101 n n 
C4' O4' GDP sing 102 n n 
C4' C3' GDP sing 103 n n 
C4' H4' GDP sing 104 n n 
O4' C1' GDP sing 105 n n 
C3' O3' GDP sing 106 n n 
C3' C2' GDP sing 107 n n 
C3' H3' GDP sing 108 n n 
O3' HO3' GDP sing 109 n n 
C2' O2' GDP sing 110 n n 
C2' C1' GDP sing 111 n n 
C2' H2' GDP sing 112 n n 
O2' HO2' GDP sing 113 n n 
C1' N9 GDP sing 114 n n 
C1' H1' GDP sing 115 n n 
N9 C8 GDP sing 116 n y 
N9 C4 GDP sing 117 n y 
C8 N7 GDP doub 118 n y 
C8 H8 GDP sing 119 n n 
N7 C5 GDP sing 120 n y 
C5 C6 GDP sing 121 n n 
C5 C4 GDP doub 122 n y 
C6 O6 GDP doub 123 n n 
C6 N1 GDP sing 124 n n 
N1 C2 GDP sing 125 n n 
N1 HN1 GDP sing 126 n n 
C2 N2 GDP sing 127 n n 
C2 N3 GDP doub 128 n n 
N2 HN21 GDP sing 129 n n 
N2 HN22 GDP sing 130 n n 
N3 C4 GDP sing 131 n n 
#
_atom_sites.entry_id                     3AB3 
_atom_sites.fract_transf_matrix[1][1]    0.019809 
_atom_sites.fract_transf_matrix[1][2]    -0.003454 
_atom_sites.fract_transf_matrix[1][3]    -0.00126 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01437 
_atom_sites.fract_transf_matrix[2][3]    -0.00292 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.01164 
_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
E 3 MG A 1 501 501 MG MG . 
F 4 GDP A 1 401 401 GDP GDP . 
G 5 ALF A 1 601 601 ALF ALF . 
H 3 MG C 1 502 502 MG MG . 
I 4 GDP C 1 402 402 GDP GDP . 
J 5 ALF C 1 602 602 ALF ALF . 
K 6 HOH A 1 2 2 HOH HOH . 
K 6 HOH A 2 3 3 HOH HOH . 
K 6 HOH A 3 5 5 HOH HOH . 
K 6 HOH A 4 6 6 HOH HOH . 
K 6 HOH A 5 7 7 HOH HOH . 
K 6 HOH A 6 8 8 HOH HOH . 
K 6 HOH A 7 9 9 HOH HOH . 
K 6 HOH A 8 13 13 HOH HOH . 
K 6 HOH A 9 378 16 HOH HOH . 
K 6 HOH A 10 379 17 HOH HOH . 
K 6 HOH A 11 380 19 HOH HOH . 
K 6 HOH A 12 381 21 HOH HOH . 
K 6 HOH A 13 382 26 HOH HOH . 
K 6 HOH A 14 383 27 HOH HOH . 
K 6 HOH A 15 384 29 HOH HOH . 
K 6 HOH A 16 385 34 HOH HOH . 
K 6 HOH A 17 386 35 HOH HOH . 
K 6 HOH A 18 387 36 HOH HOH . 
K 6 HOH A 19 388 37 HOH HOH . 
K 6 HOH A 20 389 39 HOH HOH . 
K 6 HOH A 21 390 41 HOH HOH . 
K 6 HOH A 22 391 45 HOH HOH . 
K 6 HOH A 23 392 47 HOH HOH . 
K 6 HOH A 24 393 48 HOH HOH . 
K 6 HOH A 25 394 49 HOH HOH . 
K 6 HOH A 26 395 51 HOH HOH . 
K 6 HOH A 27 396 52 HOH HOH . 
K 6 HOH A 28 397 56 HOH HOH . 
K 6 HOH A 29 398 59 HOH HOH . 
K 6 HOH A 30 399 60 HOH HOH . 
K 6 HOH A 31 400 64 HOH HOH . 
K 6 HOH A 32 402 65 HOH HOH . 
K 6 HOH A 33 403 69 HOH HOH . 
K 6 HOH A 34 404 70 HOH HOH . 
K 6 HOH A 35 405 71 HOH HOH . 
K 6 HOH A 36 406 73 HOH HOH . 
K 6 HOH A 37 407 77 HOH HOH . 
K 6 HOH A 38 408 80 HOH HOH . 
K 6 HOH A 39 409 82 HOH HOH . 
K 6 HOH A 40 410 84 HOH HOH . 
K 6 HOH A 41 411 87 HOH HOH . 
L 6 HOH B 1 234 10 HOH HOH . 
L 6 HOH B 2 235 18 HOH HOH . 
L 6 HOH B 3 236 25 HOH HOH . 
L 6 HOH B 4 237 30 HOH HOH . 
L 6 HOH B 5 238 31 HOH HOH . 
L 6 HOH B 6 239 32 HOH HOH . 
L 6 HOH B 7 240 40 HOH HOH . 
L 6 HOH B 8 241 42 HOH HOH . 
L 6 HOH B 9 242 72 HOH HOH . 
L 6 HOH B 10 243 78 HOH HOH . 
L 6 HOH B 11 244 79 HOH HOH . 
L 6 HOH B 12 245 85 HOH HOH . 
M 6 HOH C 1 1 1 HOH HOH . 
M 6 HOH C 2 4 4 HOH HOH . 
M 6 HOH C 3 11 11 HOH HOH . 
M 6 HOH C 4 12 12 HOH HOH . 
M 6 HOH C 5 14 14 HOH HOH . 
M 6 HOH C 6 15 15 HOH HOH . 
M 6 HOH C 7 378 20 HOH HOH . 
M 6 HOH C 8 379 23 HOH HOH . 
M 6 HOH C 9 380 24 HOH HOH . 
M 6 HOH C 10 381 28 HOH HOH . 
M 6 HOH C 11 382 33 HOH HOH . 
M 6 HOH C 12 383 38 HOH HOH . 
M 6 HOH C 13 384 43 HOH HOH . 
M 6 HOH C 14 385 46 HOH HOH . 
M 6 HOH C 15 386 50 HOH HOH . 
M 6 HOH C 16 387 53 HOH HOH . 
M 6 HOH C 17 388 54 HOH HOH . 
M 6 HOH C 18 389 55 HOH HOH . 
M 6 HOH C 19 390 58 HOH HOH . 
M 6 HOH C 20 391 61 HOH HOH . 
M 6 HOH C 21 392 62 HOH HOH . 
M 6 HOH C 22 393 63 HOH HOH . 
M 6 HOH C 23 394 66 HOH HOH . 
M 6 HOH C 24 395 67 HOH HOH . 
M 6 HOH C 25 396 68 HOH HOH . 
M 6 HOH C 26 397 74 HOH HOH . 
M 6 HOH C 27 398 75 HOH HOH . 
M 6 HOH C 28 399 81 HOH HOH . 
M 6 HOH C 29 400 83 HOH HOH . 
M 6 HOH C 30 401 86 HOH HOH . 
N 6 HOH D 1 234 22 HOH HOH . 
N 6 HOH D 2 235 44 HOH HOH . 
N 6 HOH D 3 236 57 HOH HOH . 
N 6 HOH D 4 237 76 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 . . . F 4 2.342 5.221 -1.348 1 25.11 ? PB GDP 401 A 1 
HETATM 2 O O1B GDP . . . F 4 3.768 5.006 -1.287 1 40.33 ? O1B GDP 401 A 1 
HETATM 3 O O2B GDP . . . F 4 1.788 5.895 0.021 1 31.83 ? O2B GDP 401 A 1 
HETATM 4 O O3B GDP . . . F 4 1.742 5.671 -2.664 1 35.18 ? O3B GDP 401 A 1 
HETATM 5 O O3A GDP . . . F 4 1.827 3.7 -1.232 1 24.22 ? O3A GDP 401 A 1 
HETATM 6 P PA GDP . . . F 4 1.204 2.846 -2.413 1 21.62 ? PA GDP 401 A 1 
HETATM 7 O O1A GDP . . . F 4 -0.054 3.494 -2.875 1 32.13 ? O1A GDP 401 A 1 
HETATM 8 O O2A GDP . . . F 4 2.244 2.744 -3.622 1 24.12 ? O2A GDP 401 A 1 
HETATM 9 O O5' GDP . . . F 4 0.881 1.377 -1.822 1 27.25 ? O5' GDP 401 A 1 
HETATM 10 C C5' GDP . . . F 4 2.136 0.728 -1.48 1 21.84 ? C5' GDP 401 A 1 
HETATM 11 C C4' GDP . . . F 4 1.938 -0.792 -1.529 1 25.67 ? C4' GDP 401 A 1 
HETATM 12 O O4' GDP . . . F 4 0.991 -1.263 -0.529 1 22.1 ? O4' GDP 401 A 1 
HETATM 13 C C3' GDP . . . F 4 1.376 -1.332 -2.843 1 24.38 ? C3' GDP 401 A 1 
HETATM 14 O O3' GDP . . . F 4 1.806 -2.473 -3.582 1 26.75 ? O3' GDP 401 A 1 
HETATM 15 C C2' GDP . . . F 4 -0.151 -1.205 -2.587 1 20.32 ? C2' GDP 401 A 1 
HETATM 16 O O2' GDP . . . F 4 -0.849 -2.156 -3.4 1 25.78 ? O2' GDP 401 A 1 
HETATM 17 C C1' GDP . . . F 4 -0.195 -1.805 -1.214 1 19.45 ? C1' GDP 401 A 1 
HETATM 18 N N9 GDP . . . F 4 -1.33 -1.404 -0.416 1 30.3 ? N9 GDP 401 A 1 
HETATM 19 C C8 GDP . . . F 4 -1.806 -0.125 -0.202 1 19.15 ? C8 GDP 401 A 1 
HETATM 20 N N7 GDP . . . F 4 -2.827 -0.165 0.587 1 25.78 ? N7 GDP 401 A 1 
HETATM 21 C C5 GDP . . . F 4 -3.066 -1.459 0.929 1 34.07 ? C5 GDP 401 A 1 
HETATM 22 C C6 GDP . . . F 4 -4.022 -2.126 1.76 1 34.55 ? C6 GDP 401 A 1 
HETATM 23 O O6 GDP . . . F 4 -4.88 -1.487 2.366 1 29.83 ? O6 GDP 401 A 1 
HETATM 24 N N1 GDP . . . F 4 -3.946 -3.493 1.856 1 31.87 ? N1 GDP 401 A 1 
HETATM 25 C C2 GDP . . . F 4 -2.968 -4.19 1.166 1 33.54 ? C2 GDP 401 A 1 
HETATM 26 N N2 GDP . . . F 4 -2.899 -5.551 1.252 1 30.17 ? N2 GDP 401 A 1 
HETATM 27 N N3 GDP . . . F 4 -2.094 -3.569 0.417 1 30.6 ? N3 GDP 401 A 1 
HETATM 28 C C4 GDP . . . F 4 -2.101 -2.253 0.274 1 27.02 ? C4 GDP 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          28 
_model_server_stats.element_count           28 
#