data_5VQ2
#
_model_server_result.job_id            XvohWyQwEZts5aJPKS_ovA 
_model_server_result.datetime_utc      '2024-11-22 04:28:46' 
_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          5vq2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    5VQ2 
#
_exptl.entry_id    5VQ2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-TRIPHOSPHATE" 
_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         120 
_cell.entry_id            5VQ2 
_cell.length_a            94.919 
_cell.length_b            94.919 
_cell.length_c            120.5 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VQ2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
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 monomeric 1 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,C,D,G 1 1 
B,E,F,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E 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 A NE2 GLN 26 A GLN 25 1_555 B NE2 GLN 26 B GLN 25 6_445 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? 
metalc ? metalc1 A OG SER 18 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc2 C O2G GTP . A GTP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc3 C O2B GTP . A GTP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc4 D MG MG . A MG 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? 
metalc ? metalc5 B OG SER 18 B SER 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc6 E O3G GTP . B GTP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc7 E O1B GTP . B GTP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc8 F MG MG . B MG 202 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
#
_chem_comp.formula           'C10 H16 N5 O14 P3' 
_chem_comp.formula_weight    523.18 
_chem_comp.id                GTP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G GTP doub 129 n n 
PG O2G GTP sing 130 n n 
PG O3G GTP sing 131 n n 
PG O3B GTP sing 132 n n 
O2G HOG2 GTP sing 133 n n 
O3G HOG3 GTP sing 134 n n 
O3B PB GTP sing 135 n n 
PB O1B GTP doub 136 n n 
PB O2B GTP sing 137 n n 
PB O3A GTP sing 138 n n 
O2B HOB2 GTP sing 139 n n 
O3A PA GTP sing 140 n n 
PA O1A GTP doub 141 n n 
PA O2A GTP sing 142 n n 
PA O5' GTP sing 143 n n 
O2A HOA2 GTP sing 144 n n 
O5' C5' GTP sing 145 n n 
C5' C4' GTP sing 146 n n 
C5' H5' GTP sing 147 n n 
C5' "H5''" GTP sing 148 n n 
C4' O4' GTP sing 149 n n 
C4' C3' GTP sing 150 n n 
C4' H4' GTP sing 151 n n 
O4' C1' GTP sing 152 n n 
C3' O3' GTP sing 153 n n 
C3' C2' GTP sing 154 n n 
C3' H3' GTP sing 155 n n 
O3' HO3' GTP sing 156 n n 
C2' O2' GTP sing 157 n n 
C2' C1' GTP sing 158 n n 
C2' H2' GTP sing 159 n n 
O2' HO2' GTP sing 160 n n 
C1' N9 GTP sing 161 n n 
C1' H1' GTP sing 162 n n 
N9 C8 GTP sing 163 n y 
N9 C4 GTP sing 164 n y 
C8 N7 GTP doub 165 n y 
C8 H8 GTP sing 166 n n 
N7 C5 GTP sing 167 n y 
C5 C6 GTP sing 168 n n 
C5 C4 GTP doub 169 n y 
C6 O6 GTP doub 170 n n 
C6 N1 GTP sing 171 n n 
N1 C2 GTP sing 172 n n 
N1 HN1 GTP sing 173 n n 
C2 N2 GTP sing 174 n n 
C2 N3 GTP doub 175 n n 
N2 HN21 GTP sing 176 n n 
N2 HN22 GTP sing 177 n n 
N3 C4 GTP sing 178 n n 
#
_atom_sites.entry_id                     5VQ2 
_atom_sites.fract_transf_matrix[1][1]    0.010535 
_atom_sites.fract_transf_matrix[1][2]    0.006083 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012165 
_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]    0.008299 
_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
C 2 GTP A 1 201 2 GTP GTP . 
D 3 MG A 1 202 1 MG MG . 
E 2 GTP B 1 201 1 GTP GTP . 
F 3 MG B 1 202 2 MG MG . 
G 4 HOH A 1 301 106 HOH HOH . 
G 4 HOH A 2 302 69 HOH HOH . 
G 4 HOH A 3 303 8 HOH HOH . 
G 4 HOH A 4 304 28 HOH HOH . 
G 4 HOH A 5 305 88 HOH HOH . 
G 4 HOH A 6 306 63 HOH HOH . 
G 4 HOH A 7 307 7 HOH HOH . 
G 4 HOH A 8 308 78 HOH HOH . 
G 4 HOH A 9 309 21 HOH HOH . 
G 4 HOH A 10 310 86 HOH HOH . 
G 4 HOH A 11 311 26 HOH HOH . 
G 4 HOH A 12 312 56 HOH HOH . 
G 4 HOH A 13 313 108 HOH HOH . 
G 4 HOH A 14 314 53 HOH HOH . 
G 4 HOH A 15 315 45 HOH HOH . 
G 4 HOH A 16 316 80 HOH HOH . 
G 4 HOH A 17 317 39 HOH HOH . 
G 4 HOH A 18 318 15 HOH HOH . 
G 4 HOH A 19 319 25 HOH HOH . 
G 4 HOH A 20 320 27 HOH HOH . 
G 4 HOH A 21 321 101 HOH HOH . 
G 4 HOH A 22 322 66 HOH HOH . 
G 4 HOH A 23 323 68 HOH HOH . 
G 4 HOH A 24 324 107 HOH HOH . 
G 4 HOH A 25 325 4 HOH HOH . 
G 4 HOH A 26 326 90 HOH HOH . 
G 4 HOH A 27 327 64 HOH HOH . 
G 4 HOH A 28 328 12 HOH HOH . 
G 4 HOH A 29 329 40 HOH HOH . 
G 4 HOH A 30 330 70 HOH HOH . 
G 4 HOH A 31 331 57 HOH HOH . 
G 4 HOH A 32 332 20 HOH HOH . 
G 4 HOH A 33 333 48 HOH HOH . 
G 4 HOH A 34 334 36 HOH HOH . 
G 4 HOH A 35 335 87 HOH HOH . 
G 4 HOH A 36 336 71 HOH HOH . 
G 4 HOH A 37 337 79 HOH HOH . 
G 4 HOH A 38 338 83 HOH HOH . 
G 4 HOH A 39 339 30 HOH HOH . 
G 4 HOH A 40 340 59 HOH HOH . 
G 4 HOH A 41 341 55 HOH HOH . 
G 4 HOH A 42 342 43 HOH HOH . 
G 4 HOH A 43 343 13 HOH HOH . 
G 4 HOH A 44 344 6 HOH HOH . 
G 4 HOH A 45 345 11 HOH HOH . 
G 4 HOH A 46 346 14 HOH HOH . 
G 4 HOH A 47 347 100 HOH HOH . 
G 4 HOH A 48 348 77 HOH HOH . 
G 4 HOH A 49 349 72 HOH HOH . 
G 4 HOH A 50 350 92 HOH HOH . 
G 4 HOH A 51 351 93 HOH HOH . 
G 4 HOH A 52 352 34 HOH HOH . 
G 4 HOH A 53 353 94 HOH HOH . 
G 4 HOH A 54 354 31 HOH HOH . 
G 4 HOH A 55 355 99 HOH HOH . 
H 4 HOH B 1 301 85 HOH HOH . 
H 4 HOH B 2 302 104 HOH HOH . 
H 4 HOH B 3 303 16 HOH HOH . 
H 4 HOH B 4 304 19 HOH HOH . 
H 4 HOH B 5 305 73 HOH HOH . 
H 4 HOH B 6 306 17 HOH HOH . 
H 4 HOH B 7 307 105 HOH HOH . 
H 4 HOH B 8 308 91 HOH HOH . 
H 4 HOH B 9 309 49 HOH HOH . 
H 4 HOH B 10 310 98 HOH HOH . 
H 4 HOH B 11 311 60 HOH HOH . 
H 4 HOH B 12 312 44 HOH HOH . 
H 4 HOH B 13 313 3 HOH HOH . 
H 4 HOH B 14 314 96 HOH HOH . 
H 4 HOH B 15 315 67 HOH HOH . 
H 4 HOH B 16 316 37 HOH HOH . 
H 4 HOH B 17 317 58 HOH HOH . 
H 4 HOH B 18 318 54 HOH HOH . 
H 4 HOH B 19 319 89 HOH HOH . 
H 4 HOH B 20 320 22 HOH HOH . 
H 4 HOH B 21 321 5 HOH HOH . 
H 4 HOH B 22 322 32 HOH HOH . 
H 4 HOH B 23 323 82 HOH HOH . 
H 4 HOH B 24 324 46 HOH HOH . 
H 4 HOH B 25 325 52 HOH HOH . 
H 4 HOH B 26 326 51 HOH HOH . 
H 4 HOH B 27 327 1 HOH HOH . 
H 4 HOH B 28 328 9 HOH HOH . 
H 4 HOH B 29 329 50 HOH HOH . 
H 4 HOH B 30 330 10 HOH HOH . 
H 4 HOH B 31 331 74 HOH HOH . 
H 4 HOH B 32 332 35 HOH HOH . 
H 4 HOH B 33 333 41 HOH HOH . 
H 4 HOH B 34 334 42 HOH HOH . 
H 4 HOH B 35 335 81 HOH HOH . 
H 4 HOH B 36 336 29 HOH HOH . 
H 4 HOH B 37 337 62 HOH HOH . 
H 4 HOH B 38 338 102 HOH HOH . 
H 4 HOH B 39 339 47 HOH HOH . 
H 4 HOH B 40 340 75 HOH HOH . 
H 4 HOH B 41 341 103 HOH HOH . 
H 4 HOH B 42 342 2 HOH HOH . 
H 4 HOH B 43 343 65 HOH HOH . 
H 4 HOH B 44 344 61 HOH HOH . 
H 4 HOH B 45 345 23 HOH HOH . 
H 4 HOH B 46 346 95 HOH HOH . 
H 4 HOH B 47 347 24 HOH HOH . 
H 4 HOH B 48 348 18 HOH HOH . 
H 4 HOH B 49 349 76 HOH HOH . 
H 4 HOH B 50 350 33 HOH HOH . 
H 4 HOH B 51 351 84 HOH HOH . 
H 4 HOH B 52 352 97 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 PG GTP . . . C 2 -8.212 -42.142 21.015 1 71.41 ? PG GTP 201 A 1 
HETATM 2 O O1G GTP . . . C 2 -9.092 -43.319 20.624 1 72.16 ? O1G GTP 201 A 1 
HETATM 3 O O2G GTP . . . C 2 -8.988 -40.92 21.477 1 62.1 ? O2G GTP 201 A 1 
HETATM 4 O O3G GTP . . . C 2 -7.05 -42.545 21.917 1 66.85 ? O3G GTP 201 A 1 
HETATM 5 O O3B GTP . . . C 2 -7.451 -41.661 19.664 1 36.84 ? O3B GTP 201 A 1 
HETATM 6 P PB GTP . . . C 2 -8.133 -40.825 18.476 1 24.07 ? PB GTP 201 A 1 
HETATM 7 O O1B GTP . . . C 2 -8.586 -41.787 17.393 1 24.26 ? O1B GTP 201 A 1 
HETATM 8 O O2B GTP . . . C 2 -9.141 -39.857 18.97 1 25.75 ? O2B GTP 201 A 1 
HETATM 9 O O3A GTP . . . C 2 -6.818 -40.103 17.84 1 22.72 ? O3A GTP 201 A 1 
HETATM 10 P PA GTP . . . C 2 -6.42 -38.554 17.923 1 25.59 ? PA GTP 201 A 1 
HETATM 11 O O1A GTP . . . C 2 -7.506 -37.695 17.301 1 25.26 ? O1A GTP 201 A 1 
HETATM 12 O O2A GTP . . . C 2 -5.964 -38.308 19.326 1 27.17 ? O2A GTP 201 A 1 
HETATM 13 O O5' GTP . . . C 2 -5.176 -38.524 16.938 1 24.82 ? O5' GTP 201 A 1 
HETATM 14 C C5' GTP . . . C 2 -4.085 -39.409 17.208 1 26.01 ? C5' GTP 201 A 1 
HETATM 15 C C4' GTP . . . C 2 -2.791 -38.814 16.646 1 25.95 ? C4' GTP 201 A 1 
HETATM 16 O O4' GTP . . . C 2 -2.812 -38.753 15.219 1 22.24 ? O4' GTP 201 A 1 
HETATM 17 C C3' GTP . . . C 2 -2.579 -37.377 17.103 1 25.62 ? C3' GTP 201 A 1 
HETATM 18 O O3' GTP . . . C 2 -1.176 -37.183 17.242 1 28.01 ? O3' GTP 201 A 1 
HETATM 19 C C2' GTP . . . C 2 -3.061 -36.523 15.965 1 25.33 ? C2' GTP 201 A 1 
HETATM 20 O O2' GTP . . . C 2 -2.385 -35.277 15.848 1 26.94 ? O2' GTP 201 A 1 
HETATM 21 C C1' GTP . . . C 2 -2.69 -37.4 14.782 1 23.59 ? C1' GTP 201 A 1 
HETATM 22 N N9 GTP . . . C 2 -3.603 -37.211 13.648 1 20.09 ? N9 GTP 201 A 1 
HETATM 23 C C8 GTP . . . C 2 -4.941 -37.307 13.698 1 20.55 ? C8 GTP 201 A 1 
HETATM 24 N N7 GTP . . . C 2 -5.486 -37.138 12.471 1 20.46 ? N7 GTP 201 A 1 
HETATM 25 C C5 GTP . . . C 2 -4.462 -36.886 11.64 1 19.68 ? C5 GTP 201 A 1 
HETATM 26 C C6 GTP . . . C 2 -4.329 -36.644 10.212 1 18.85 ? C6 GTP 201 A 1 
HETATM 27 O O6 GTP . . . C 2 -5.341 -36.596 9.503 1 18.45 ? O6 GTP 201 A 1 
HETATM 28 N N1 GTP . . . C 2 -3.102 -36.436 9.719 1 20.52 ? N1 GTP 201 A 1 
HETATM 29 C C2 GTP . . . C 2 -2.007 -36.495 10.522 1 20.09 ? C2 GTP 201 A 1 
HETATM 30 N N2 GTP . . . C 2 -0.815 -36.285 9.982 1 20.79 ? N2 GTP 201 A 1 
HETATM 31 N N3 GTP . . . C 2 -2.047 -36.771 11.847 1 20.76 ? N3 GTP 201 A 1 
HETATM 32 C C4 GTP . . . C 2 -3.229 -36.933 12.436 1 18.83 ? C4 GTP 201 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           32 
#