data_1AGR
#
_model_server_result.job_id            IsVZ0o8YDAq8RJQ2eaNreQ 
_model_server_result.datetime_utc      '2024-11-08 12:52:34' 
_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          1agr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":355}' 
#
_entry.id    1AGR 
#
_exptl.entry_id    1AGR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            1AGR 
_cell.length_a            164 
_cell.length_b            97.2 
_cell.length_c            110 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1AGR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,H,M,O 1 1 
B,D,I,J,K,L,N,P 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
? 5 G N N 
? 5 K 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
covale ? covale1 G O3B GDP . A GDP 355 1_555 F F1 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
covale ? covale2 K O3B GDP . D GDP 355 1_555 J F1 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc1 A OG SER 46 A SER 47 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc2 A NH2 ARG 177 A ARG 178 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.689 ? 
metalc ? metalc3 A OG1 THR 180 A THR 181 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? 
metalc ? metalc4 G O2B GDP . A GDP 355 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc5 G O3B GDP . A GDP 355 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc6 G O2B GDP . A GDP 355 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.581 ? 
metalc ? metalc7 E MG MG . A MG 356 1_555 F F2 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? 
metalc ? metalc8 E MG MG . A MG 356 1_555 F F3 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc9 E MG MG . A MG 356 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.297 ? 
metalc ? metalc10 E MG MG . A MG 356 1_555 M O HOH . A HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc11 E MG MG . A MG 356 1_555 M O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc12 F AL ALF . A ALF 357 1_555 M O HOH . A HOH 359 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc13 B OG SER 46 D SER 47 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
metalc ? metalc14 B NH2 ARG 177 D ARG 178 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.668 ? 
metalc ? metalc15 B OG1 THR 180 D THR 181 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc16 K O2B GDP . D GDP 355 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc17 K O3B GDP . D GDP 355 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc18 K O2B GDP . D GDP 355 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.613 ? 
metalc ? metalc19 I MG MG . D MG 356 1_555 J F3 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc20 I MG MG . D MG 356 1_555 J F2 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? 
metalc ? metalc21 I MG MG . D MG 356 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.326 ? 
metalc ? metalc22 I MG MG . D MG 356 1_555 N O HOH . D HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc23 I MG MG . D MG 356 1_555 N O HOH . D HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc24 J AL ALF . D ALF 357 1_555 N O HOH . D HOH 360 1_555 ? ? ? D ? ? ? ? ? ? ? ? 2.005 ? 
#
_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 107 n n 
PB O2B GDP sing 108 n n 
PB O3B GDP sing 109 n n 
PB O3A GDP sing 110 n n 
O2B HOB2 GDP sing 111 n n 
O3B HOB3 GDP sing 112 n n 
O3A PA GDP sing 113 n n 
PA O1A GDP doub 114 n n 
PA O2A GDP sing 115 n n 
PA O5' GDP sing 116 n n 
O2A HOA2 GDP sing 117 n n 
O5' C5' GDP sing 118 n n 
C5' C4' GDP sing 119 n n 
C5' H5' GDP sing 120 n n 
C5' "H5''" GDP sing 121 n n 
C4' O4' GDP sing 122 n n 
C4' C3' GDP sing 123 n n 
C4' H4' GDP sing 124 n n 
O4' C1' GDP sing 125 n n 
C3' O3' GDP sing 126 n n 
C3' C2' GDP sing 127 n n 
C3' H3' GDP sing 128 n n 
O3' HO3' GDP sing 129 n n 
C2' O2' GDP sing 130 n n 
C2' C1' GDP sing 131 n n 
C2' H2' GDP sing 132 n n 
O2' HO2' GDP sing 133 n n 
C1' N9 GDP sing 134 n n 
C1' H1' GDP sing 135 n n 
N9 C8 GDP sing 136 n y 
N9 C4 GDP sing 137 n y 
C8 N7 GDP doub 138 n y 
C8 H8 GDP sing 139 n n 
N7 C5 GDP sing 140 n y 
C5 C6 GDP sing 141 n n 
C5 C4 GDP doub 142 n y 
C6 O6 GDP doub 143 n n 
C6 N1 GDP sing 144 n n 
N1 C2 GDP sing 145 n n 
N1 HN1 GDP sing 146 n n 
C2 N2 GDP sing 147 n n 
C2 N3 GDP doub 148 n n 
N2 HN21 GDP sing 149 n n 
N2 HN22 GDP sing 150 n n 
N3 C4 GDP sing 151 n n 
#
_atom_sites.entry_id                     1AGR 
_atom_sites.fract_transf_matrix[1][1]    0.006098 
_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]    0.010288 
_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]    0.009091 
_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 1 356 356 MG MG . 
F 4 ALF A 1 357 357 ALF ALF . 
G 5 GDP A 1 355 355 GDP GDP . 
H 6 CIT A 1 358 358 CIT CIT . 
I 3 MG D 1 356 356 MG MG . 
J 4 ALF D 1 357 357 ALF ALF . 
K 5 GDP D 1 355 355 GDP GDP . 
L 6 CIT D 1 358 358 CIT CIT . 
M 7 HOH A 1 359 357 HOH HOH A 
M 7 HOH A 2 360 402 HOH HOH . 
M 7 HOH A 3 361 403 HOH HOH . 
M 7 HOH A 4 362 406 HOH HOH . 
M 7 HOH A 5 363 409 HOH HOH . 
M 7 HOH A 6 364 410 HOH HOH . 
M 7 HOH A 7 365 412 HOH HOH . 
M 7 HOH A 8 366 414 HOH HOH . 
M 7 HOH A 9 367 415 HOH HOH . 
M 7 HOH A 10 368 421 HOH HOH . 
M 7 HOH A 11 369 424 HOH HOH . 
M 7 HOH A 12 370 436 HOH HOH . 
M 7 HOH A 13 371 438 HOH HOH . 
M 7 HOH A 14 372 442 HOH HOH . 
M 7 HOH A 15 373 454 HOH HOH . 
M 7 HOH A 16 374 455 HOH HOH . 
M 7 HOH A 17 375 457 HOH HOH . 
M 7 HOH A 18 376 460 HOH HOH . 
M 7 HOH A 19 377 461 HOH HOH . 
M 7 HOH A 20 378 470 HOH HOH . 
M 7 HOH A 21 379 471 HOH HOH . 
M 7 HOH A 22 380 474 HOH HOH . 
M 7 HOH A 23 381 476 HOH HOH . 
M 7 HOH A 24 382 480 HOH HOH . 
M 7 HOH A 25 383 485 HOH HOH . 
M 7 HOH A 26 384 434 HOH HOH . 
N 7 HOH D 1 359 434 HOH HOH . 
N 7 HOH D 2 360 357 HOH HOH D 
N 7 HOH D 3 361 402 HOH HOH . 
N 7 HOH D 4 362 403 HOH HOH . 
N 7 HOH D 5 363 406 HOH HOH . 
N 7 HOH D 6 364 409 HOH HOH . 
N 7 HOH D 7 365 410 HOH HOH . 
N 7 HOH D 8 366 412 HOH HOH . 
N 7 HOH D 9 367 414 HOH HOH . 
N 7 HOH D 10 368 415 HOH HOH . 
N 7 HOH D 11 369 421 HOH HOH . 
N 7 HOH D 12 370 424 HOH HOH . 
N 7 HOH D 13 371 436 HOH HOH . 
N 7 HOH D 14 372 438 HOH HOH . 
N 7 HOH D 15 373 442 HOH HOH . 
N 7 HOH D 16 374 454 HOH HOH . 
N 7 HOH D 17 375 455 HOH HOH . 
N 7 HOH D 18 376 457 HOH HOH . 
N 7 HOH D 19 377 460 HOH HOH . 
N 7 HOH D 20 378 461 HOH HOH . 
N 7 HOH D 21 379 470 HOH HOH . 
N 7 HOH D 22 380 471 HOH HOH . 
N 7 HOH D 23 381 474 HOH HOH . 
N 7 HOH D 24 382 476 HOH HOH . 
N 7 HOH D 25 383 480 HOH HOH . 
N 7 HOH D 26 384 485 HOH HOH . 
O 7 HOH E 1 206 413 HOH HOH . 
O 7 HOH E 2 207 469 HOH HOH . 
O 7 HOH E 3 208 481 HOH HOH . 
P 7 HOH H 1 206 413 HOH HOH . 
P 7 HOH H 2 207 469 HOH HOH . 
P 7 HOH H 3 208 481 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 . . . G 5 26.249 8.5 41.19 1 16.89 ? PB GDP 355 A 1 
HETATM 2 O O1B GDP . . . G 5 27.682 8.001 41.035 1 7.85 ? O1B GDP 355 A 1 
HETATM 3 O O2B GDP . . . G 5 25.54 8.267 42.464 1 2 ? O2B GDP 355 A 1 
HETATM 4 O O3B GDP . . . G 5 26.03 9.936 40.847 1 28.47 ? O3B GDP 355 A 1 
HETATM 5 O O3A GDP . . . G 5 25.407 7.707 40.001 1 11.47 ? O3A GDP 355 A 1 
HETATM 6 P PA GDP . . . G 5 23.879 7.317 40.296 1 19.25 ? PA GDP 355 A 1 
HETATM 7 O O1A GDP . . . G 5 23.992 6.346 41.388 1 28.3 ? O1A GDP 355 A 1 
HETATM 8 O O2A GDP . . . G 5 22.912 8.357 40.638 1 20.32 ? O2A GDP 355 A 1 
HETATM 9 O O5' GDP . . . G 5 23.434 6.659 38.936 1 7.94 ? O5' GDP 355 A 1 
HETATM 10 C C5' GDP . . . G 5 23.328 7.327 37.761 1 7.85 ? C5' GDP 355 A 1 
HETATM 11 C C4' GDP . . . G 5 22.069 6.92 36.991 1 11.29 ? C4' GDP 355 A 1 
HETATM 12 O O4' GDP . . . G 5 22.253 5.745 36.227 1 18.19 ? O4' GDP 355 A 1 
HETATM 13 C C3' GDP . . . G 5 20.843 6.694 37.77 1 15.42 ? C3' GDP 355 A 1 
HETATM 14 O O3' GDP . . . G 5 19.757 6.912 36.932 1 17.54 ? O3' GDP 355 A 1 
HETATM 15 C C2' GDP . . . G 5 20.882 5.155 37.945 1 22.21 ? C2' GDP 355 A 1 
HETATM 16 O O2' GDP . . . G 5 19.576 4.609 37.805 1 28.15 ? O2' GDP 355 A 1 
HETATM 17 C C1' GDP . . . G 5 21.493 4.605 36.712 1 20.89 ? C1' GDP 355 A 1 
HETATM 18 N N9 GDP . . . G 5 22.47 3.421 36.778 1 25.79 ? N9 GDP 355 A 1 
HETATM 19 C C8 GDP . . . G 5 23.516 3.128 37.589 1 19.67 ? C8 GDP 355 A 1 
HETATM 20 N N7 GDP . . . G 5 24.248 2.118 37.279 1 12.97 ? N7 GDP 355 A 1 
HETATM 21 C C5 GDP . . . G 5 23.622 1.667 36.15 1 21.76 ? C5 GDP 355 A 1 
HETATM 22 C C6 GDP . . . G 5 23.946 0.555 35.318 1 25.43 ? C6 GDP 355 A 1 
HETATM 23 O O6 GDP . . . G 5 24.867 -0.254 35.472 1 21.2 ? O6 GDP 355 A 1 
HETATM 24 N N1 GDP . . . G 5 23.046 0.457 34.234 1 23.29 ? N1 GDP 355 A 1 
HETATM 25 C C2 GDP . . . G 5 21.976 1.323 33.988 1 23.5 ? C2 GDP 355 A 1 
HETATM 26 N N2 GDP . . . G 5 21.23 1.172 32.93 1 19.31 ? N2 GDP 355 A 1 
HETATM 27 N N3 GDP . . . G 5 21.671 2.339 34.769 1 26.6 ? N3 GDP 355 A 1 
HETATM 28 C C4 GDP . . . G 5 22.538 2.446 35.835 1 25.71 ? C4 GDP 355 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#