data_6GVN
#
_model_server_result.job_id            7XVY2tQWhrpFUm0THXMNPA 
_model_server_result.datetime_utc      '2024-11-25 11:28:58' 
_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          6gvn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    6GVN 
#
_exptl.entry_id    6GVN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          4 
_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          99 
_cell.angle_gamma         90 
_cell.entry_id            6GVN 
_cell.length_a            73.1 
_cell.length_b            84.26 
_cell.length_c            81.98 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GVN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 monomeric 1 software_defined_assembly 1 
PISA dimeric 2 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,D,E,F,L 1 1 
B,C,G,H,I,J,K,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 D N N 
? 4 G 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 D O2G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? 
metalc ? metalc2 D O1B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? 
metalc ? metalc3 E MG MG . A MG 502 1_555 L O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? 
metalc ? metalc4 E MG MG . A MG 502 1_555 L O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc5 G O2G GTP . B GTP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? 
metalc ? metalc6 G O1B GTP . B GTP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
#
_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 142 n n 
PG O2G GTP sing 143 n n 
PG O3G GTP sing 144 n n 
PG O3B GTP sing 145 n n 
O2G HOG2 GTP sing 146 n n 
O3G HOG3 GTP sing 147 n n 
O3B PB GTP sing 148 n n 
PB O1B GTP doub 149 n n 
PB O2B GTP sing 150 n n 
PB O3A GTP sing 151 n n 
O2B HOB2 GTP sing 152 n n 
O3A PA GTP sing 153 n n 
PA O1A GTP doub 154 n n 
PA O2A GTP sing 155 n n 
PA O5' GTP sing 156 n n 
O2A HOA2 GTP sing 157 n n 
O5' C5' GTP sing 158 n n 
C5' C4' GTP sing 159 n n 
C5' H5' GTP sing 160 n n 
C5' "H5''" GTP sing 161 n n 
C4' O4' GTP sing 162 n n 
C4' C3' GTP sing 163 n n 
C4' H4' GTP sing 164 n n 
O4' C1' GTP sing 165 n n 
C3' O3' GTP sing 166 n n 
C3' C2' GTP sing 167 n n 
C3' H3' GTP sing 168 n n 
O3' HO3' GTP sing 169 n n 
C2' O2' GTP sing 170 n n 
C2' C1' GTP sing 171 n n 
C2' H2' GTP sing 172 n n 
O2' HO2' GTP sing 173 n n 
C1' N9 GTP sing 174 n n 
C1' H1' GTP sing 175 n n 
N9 C8 GTP sing 176 n y 
N9 C4 GTP sing 177 n y 
C8 N7 GTP doub 178 n y 
C8 H8 GTP sing 179 n n 
N7 C5 GTP sing 180 n y 
C5 C6 GTP sing 181 n n 
C5 C4 GTP doub 182 n y 
C6 O6 GTP doub 183 n n 
C6 N1 GTP sing 184 n n 
N1 C2 GTP sing 185 n n 
N1 HN1 GTP sing 186 n n 
C2 N2 GTP sing 187 n n 
C2 N3 GTP doub 188 n n 
N2 HN21 GTP sing 189 n n 
N2 HN22 GTP sing 190 n n 
N3 C4 GTP sing 191 n n 
#
_atom_sites.entry_id                     6GVN 
_atom_sites.fract_transf_matrix[1][1]    0.01368 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002167 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011868 
_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]    0.01235 
_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 4 GTP A 1 501 501 GTP GTP . 
E 5 MG A 1 502 502 MG MG . 
F 6 SO4 A 1 503 1 SO4 SO4 . 
G 4 GTP B 1 501 501 GTP GTP . 
H 5 MG B 1 502 502 MG MG . 
I 7 MES B 1 503 1 MES MES . 
J 8 GOL B 1 504 1 GOL GOL . 
K 8 GOL F 1 201 2 GOL GOL . 
L 9 HOH A 1 601 98 HOH HOH . 
L 9 HOH A 2 602 511 HOH HOH . 
L 9 HOH A 3 603 512 HOH HOH . 
L 9 HOH A 4 604 94 HOH HOH . 
L 9 HOH A 5 605 109 HOH HOH . 
L 9 HOH A 6 606 105 HOH HOH . 
L 9 HOH A 7 607 101 HOH HOH . 
L 9 HOH A 8 608 43 HOH HOH . 
L 9 HOH A 9 609 4 HOH HOH . 
L 9 HOH A 10 610 93 HOH HOH . 
L 9 HOH A 11 611 97 HOH HOH . 
L 9 HOH A 12 612 2 HOH HOH . 
L 9 HOH A 13 613 21 HOH HOH . 
L 9 HOH A 14 614 27 HOH HOH . 
L 9 HOH A 15 615 48 HOH HOH . 
L 9 HOH A 16 616 45 HOH HOH . 
L 9 HOH A 17 617 29 HOH HOH . 
L 9 HOH A 18 618 7 HOH HOH . 
L 9 HOH A 19 619 77 HOH HOH . 
L 9 HOH A 20 620 100 HOH HOH . 
L 9 HOH A 21 621 89 HOH HOH . 
L 9 HOH A 22 622 72 HOH HOH . 
L 9 HOH A 23 623 70 HOH HOH . 
L 9 HOH A 24 624 14 HOH HOH . 
L 9 HOH A 25 625 53 HOH HOH . 
L 9 HOH A 26 626 92 HOH HOH . 
L 9 HOH A 27 627 513 HOH HOH . 
L 9 HOH A 28 628 69 HOH HOH . 
L 9 HOH A 29 629 87 HOH HOH . 
L 9 HOH A 30 630 108 HOH HOH . 
L 9 HOH A 31 631 102 HOH HOH . 
L 9 HOH A 32 632 51 HOH HOH . 
L 9 HOH A 33 633 110 HOH HOH . 
L 9 HOH A 34 634 5 HOH HOH . 
L 9 HOH A 35 635 104 HOH HOH . 
L 9 HOH A 36 636 62 HOH HOH . 
L 9 HOH A 37 637 31 HOH HOH . 
L 9 HOH A 38 638 83 HOH HOH . 
L 9 HOH A 39 639 34 HOH HOH . 
L 9 HOH A 40 640 57 HOH HOH . 
L 9 HOH A 41 641 41 HOH HOH . 
L 9 HOH A 42 642 1 HOH HOH . 
L 9 HOH A 43 643 71 HOH HOH . 
L 9 HOH A 44 644 42 HOH HOH . 
L 9 HOH A 45 645 54 HOH HOH . 
L 9 HOH A 46 646 37 HOH HOH . 
L 9 HOH A 47 647 75 HOH HOH . 
L 9 HOH A 48 648 80 HOH HOH . 
L 9 HOH A 49 649 47 HOH HOH . 
L 9 HOH A 50 650 24 HOH HOH . 
L 9 HOH A 51 651 81 HOH HOH . 
M 9 HOH B 1 601 11 HOH HOH . 
M 9 HOH B 2 602 111 HOH HOH . 
M 9 HOH B 3 603 73 HOH HOH . 
M 9 HOH B 4 604 112 HOH HOH . 
M 9 HOH B 5 605 103 HOH HOH . 
M 9 HOH B 6 606 10 HOH HOH . 
M 9 HOH B 7 607 95 HOH HOH . 
M 9 HOH B 8 608 86 HOH HOH . 
M 9 HOH B 9 609 22 HOH HOH . 
M 9 HOH B 10 610 35 HOH HOH . 
M 9 HOH B 11 611 26 HOH HOH . 
M 9 HOH B 12 612 38 HOH HOH . 
M 9 HOH B 13 613 32 HOH HOH . 
M 9 HOH B 14 614 3 HOH HOH . 
M 9 HOH B 15 615 74 HOH HOH . 
M 9 HOH B 16 616 49 HOH HOH . 
M 9 HOH B 17 617 33 HOH HOH . 
M 9 HOH B 18 618 88 HOH HOH . 
M 9 HOH B 19 619 15 HOH HOH . 
M 9 HOH B 20 620 85 HOH HOH . 
M 9 HOH B 21 621 13 HOH HOH . 
M 9 HOH B 22 622 96 HOH HOH . 
M 9 HOH B 23 623 107 HOH HOH . 
M 9 HOH B 24 624 6 HOH HOH . 
M 9 HOH B 25 625 20 HOH HOH . 
M 9 HOH B 26 626 78 HOH HOH . 
M 9 HOH B 27 627 55 HOH HOH . 
M 9 HOH B 28 628 76 HOH HOH . 
M 9 HOH B 29 629 17 HOH HOH . 
M 9 HOH B 30 630 12 HOH HOH . 
M 9 HOH B 31 631 44 HOH HOH . 
M 9 HOH B 32 632 16 HOH HOH . 
M 9 HOH B 33 633 59 HOH HOH . 
M 9 HOH B 34 634 79 HOH HOH . 
M 9 HOH B 35 635 39 HOH HOH . 
M 9 HOH B 36 636 90 HOH HOH . 
M 9 HOH B 37 637 36 HOH HOH . 
M 9 HOH B 38 638 106 HOH HOH . 
M 9 HOH B 39 639 52 HOH HOH . 
M 9 HOH B 40 640 63 HOH HOH . 
M 9 HOH B 41 641 18 HOH HOH . 
M 9 HOH B 42 642 66 HOH HOH . 
M 9 HOH B 43 643 25 HOH HOH . 
M 9 HOH B 44 644 50 HOH HOH . 
M 9 HOH B 45 645 58 HOH HOH . 
M 9 HOH B 46 646 23 HOH HOH . 
N 9 HOH F 1 301 30 HOH HOH . 
N 9 HOH F 2 302 99 HOH HOH . 
N 9 HOH F 3 303 84 HOH HOH . 
N 9 HOH F 4 304 91 HOH HOH . 
N 9 HOH F 5 305 65 HOH HOH . 
N 9 HOH F 6 306 9 HOH HOH . 
N 9 HOH F 7 307 67 HOH HOH . 
N 9 HOH F 8 308 82 HOH HOH . 
N 9 HOH F 9 309 46 HOH HOH . 
N 9 HOH F 10 310 68 HOH HOH . 
N 9 HOH F 11 311 60 HOH HOH . 
N 9 HOH F 12 312 8 HOH HOH . 
N 9 HOH F 13 313 64 HOH HOH . 
N 9 HOH F 14 314 28 HOH HOH . 
N 9 HOH F 15 315 61 HOH HOH . 
N 9 HOH F 16 316 19 HOH HOH . 
N 9 HOH F 17 317 56 HOH HOH . 
N 9 HOH F 18 318 40 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 . . . G 4 29.841 -8.784 -14.495 1 64.02 ? PG GTP 501 B 1 
HETATM 2 O O1G GTP . . . G 4 28.569 -8.851 -15.376 1 67.78 ? O1G GTP 501 B 1 
HETATM 3 O O2G GTP . . . G 4 30.676 -10.105 -14.551 1 65.95 ? O2G GTP 501 B 1 
HETATM 4 O O3G GTP . . . G 4 30.647 -7.588 -14.866 1 61.37 ? O3G GTP 501 B 1 
HETATM 5 O O3B GTP . . . G 4 29.306 -8.407 -13.044 1 54.02 ? O3B GTP 501 B 1 
HETATM 6 P PB GTP . . . G 4 28.654 -9.328 -11.927 1 43.96 ? PB GTP 501 B 1 
HETATM 7 O O1B GTP . . . G 4 27.983 -10.465 -12.586 1 47.49 ? O1B GTP 501 B 1 
HETATM 8 O O2B GTP . . . G 4 27.703 -8.498 -11.113 1 41.24 ? O2B GTP 501 B 1 
HETATM 9 O O3A GTP . . . G 4 29.894 -9.794 -11.04 1 42.15 ? O3A GTP 501 B 1 
HETATM 10 P PA GTP . . . G 4 30.206 -10.724 -9.785 1 41.48 ? PA GTP 501 B 1 
HETATM 11 O O1A GTP . . . G 4 30.654 -12.058 -10.257 1 40.67 ? O1A GTP 501 B 1 
HETATM 12 O O2A GTP . . . G 4 28.933 -10.82 -8.978 1 40.15 ? O2A GTP 501 B 1 
HETATM 13 O O5' GTP . . . G 4 31.248 -9.88 -8.875 1 43.21 ? O5' GTP 501 B 1 
HETATM 14 C C5' GTP . . . G 4 32.63 -10.244 -8.682 1 44.67 ? C5' GTP 501 B 1 
HETATM 15 C C4' GTP . . . G 4 32.919 -10.215 -7.2 1 46.21 ? C4' GTP 501 B 1 
HETATM 16 O O4' GTP . . . G 4 31.876 -10.912 -6.476 1 46.76 ? O4' GTP 501 B 1 
HETATM 17 C C3' GTP . . . G 4 34.237 -10.858 -6.774 1 47.44 ? C3' GTP 501 B 1 
HETATM 18 O O3' GTP . . . G 4 34.875 -10.122 -5.734 1 49.27 ? O3' GTP 501 B 1 
HETATM 19 C C2' GTP . . . G 4 33.813 -12.265 -6.344 1 46.28 ? C2' GTP 501 B 1 
HETATM 20 O O2' GTP . . . G 4 34.711 -12.785 -5.371 1 45.08 ? O2' GTP 501 B 1 
HETATM 21 C C1' GTP . . . G 4 32.42 -12.004 -5.755 1 45.75 ? C1' GTP 501 B 1 
HETATM 22 N N9 GTP . . . G 4 31.47 -13.142 -5.846 1 43.12 ? N9 GTP 501 B 1 
HETATM 23 C C8 GTP . . . G 4 30.946 -13.703 -6.989 1 42.72 ? C8 GTP 501 B 1 
HETATM 24 N N7 GTP . . . G 4 30.046 -14.633 -6.76 1 41.85 ? N7 GTP 501 B 1 
HETATM 25 C C5 GTP . . . G 4 29.97 -14.698 -5.378 1 41.07 ? C5 GTP 501 B 1 
HETATM 26 C C6 GTP . . . G 4 29.182 -15.532 -4.495 1 40.32 ? C6 GTP 501 B 1 
HETATM 27 O O6 GTP . . . G 4 28.299 -16.33 -4.808 1 41.6 ? O6 GTP 501 B 1 
HETATM 28 N N1 GTP . . . G 4 29.493 -15.329 -3.163 1 37.43 ? N1 GTP 501 B 1 
HETATM 29 C C2 GTP . . . G 4 30.419 -14.438 -2.693 1 35.71 ? C2 GTP 501 B 1 
HETATM 30 N N2 GTP . . . G 4 30.661 -14.462 -1.385 1 35.01 ? N2 GTP 501 B 1 
HETATM 31 N N3 GTP . . . G 4 31.116 -13.615 -3.478 1 37.26 ? N3 GTP 501 B 1 
HETATM 32 C C4 GTP . . . G 4 30.857 -13.797 -4.798 1 40.58 ? C4 GTP 501 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           32 
#