data_6DHM
#
_model_server_result.job_id            szq9yKiyGQi1FmmqrMBHWQ 
_model_server_result.datetime_utc      '2024-11-06 00:25:44' 
_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          6dhm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"IA","auth_seq_id":604}' 
#
_entry.id    6DHM 
#
_exptl.entry_id    6DHM 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          101.55 
_cell.angle_gamma         90 
_cell.entry_id            6DHM 
_cell.length_a            121.11 
_cell.length_b            98.76 
_cell.length_c            165.64 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DHM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 I N N 
? 4 N N N 
? 4 S N N 
? 4 X N N 
? 4 CA N N 
? 4 IA 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 NE2 HIS 138 A HIS 57 1_555 Y ZN ZN . D ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc2 A OE1 GLU 232 A GLU 151 1_555 J ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? 
metalc ? metalc3 A NE2 HIS 290 A HIS 209 1_555 K ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc4 A NE2 HIS 531 A HIS 450 1_555 K ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? 
metalc ? metalc5 I O1B GTP . A GTP 603 1_555 K ZN ZN . A ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc6 J ZN ZN . A ZN 604 1_555 D NE2 HIS 138 D HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc7 B NE2 HIS 138 B HIS 57 1_555 DA ZN ZN . E ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc8 B OE1 GLU 232 B GLU 151 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc9 B OE2 GLU 232 B GLU 151 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
metalc ? metalc10 B NE2 HIS 290 B HIS 209 1_555 P ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc11 B NE2 HIS 531 B HIS 450 1_555 P ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc12 N O1B GTP . B GTP 603 1_555 P ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc13 O ZN ZN . B ZN 604 1_555 E NE2 HIS 138 E HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc14 C NE2 HIS 138 C HIS 57 1_555 FA ZN ZN . F ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc15 C OE1 GLU 232 C GLU 151 1_555 T ZN ZN . C ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc16 C OE2 GLU 232 C GLU 151 1_555 T ZN ZN . C ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc17 C NE2 HIS 290 C HIS 209 1_555 U ZN ZN . C ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc18 C NE2 HIS 531 C HIS 450 1_555 U ZN ZN . C ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc19 S O2B GTP . C GTP 603 1_555 U ZN ZN . C ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc20 T ZN ZN . C ZN 604 1_555 F NE2 HIS 138 F HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc21 D OE1 GLU 232 D GLU 151 1_555 Y ZN ZN . D ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc22 D OE2 GLU 232 D GLU 151 1_555 Y ZN ZN . D ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc23 D NE2 HIS 290 D HIS 209 1_555 Z ZN ZN . D ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc24 D NE2 HIS 531 D HIS 450 1_555 Z ZN ZN . D ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc25 X O2B GTP . D GTP 603 1_555 Z ZN ZN . D ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc26 E OE1 GLU 232 E GLU 151 1_555 DA ZN ZN . E ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc27 E OE2 GLU 232 E GLU 151 1_555 DA ZN ZN . E ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc28 E NE2 HIS 290 E HIS 209 1_555 EA ZN ZN . E ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc29 E NE2 HIS 531 E HIS 450 1_555 EA ZN ZN . E ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc30 CA O2B GTP . E GTP 603 1_555 EA ZN ZN . E ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc31 F OE1 GLU 232 F GLU 151 1_555 FA ZN ZN . F ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc32 F OE2 GLU 232 F GLU 151 1_555 FA ZN ZN . F ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc33 F NE2 HIS 290 F HIS 209 1_555 JA ZN ZN . F ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc34 F NE2 HIS 531 F HIS 450 1_555 JA ZN ZN . F ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc35 IA O1B GTP . F GTP 604 1_555 JA ZN ZN . F ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
#
_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                     6DHM 
_atom_sites.fract_transf_matrix[1][1]    0.008257 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001687 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010126 
_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]    0.006162 
_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
G 2 GLU A 1 601 502 GLU GLU . 
H 3 NDP A 1 602 552 NDP NDP . 
I 4 GTP A 1 603 503 GTP GTP . 
J 5 ZN A 1 604 504 ZN ZN . 
K 5 ZN A 1 605 505 ZN ZN . 
L 2 GLU B 1 601 502 GLU GLU . 
M 3 NDP B 1 602 552 NDP NDP . 
N 4 GTP B 1 603 503 GTP GTP . 
O 5 ZN B 1 604 504 ZN ZN . 
P 5 ZN B 1 605 505 ZN ZN . 
Q 2 GLU C 1 601 502 GLU GLU . 
R 3 NDP C 1 602 552 NDP NDP . 
S 4 GTP C 1 603 503 GTP GTP . 
T 5 ZN C 1 604 504 ZN ZN . 
U 5 ZN C 1 605 506 ZN ZN . 
V 2 GLU D 1 601 502 GLU GLU . 
W 3 NDP D 1 602 552 NDP NDP . 
X 4 GTP D 1 603 503 GTP GTP . 
Y 5 ZN D 1 604 504 ZN ZN . 
Z 5 ZN D 1 605 505 ZN ZN . 
AA 2 GLU E 1 601 502 GLU GLU . 
BA 3 NDP E 1 602 552 NDP NDP . 
CA 4 GTP E 1 603 503 GTP GTP . 
DA 5 ZN E 1 604 504 ZN ZN . 
EA 5 ZN E 1 605 505 ZN ZN . 
FA 5 ZN F 1 601 505 ZN ZN . 
GA 2 GLU F 1 602 502 GLU GLU . 
HA 3 NDP F 1 603 552 NDP NDP . 
IA 4 GTP F 1 604 503 GTP GTP . 
JA 5 ZN F 1 605 504 ZN ZN . 
#
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 . . . IA 4 5.582 -17.727 48.933 1 35.81 ? PG GTP 604 F 1 
HETATM 2 O O1G GTP . . . IA 4 4.628 -17.502 47.767 1 25.59 ? O1G GTP 604 F 1 
HETATM 3 O O2G GTP . . . IA 4 6.86 -18.344 48.456 1 22.28 ? O2G GTP 604 F 1 
HETATM 4 O O3G GTP . . . IA 4 4.975 -18.614 50.025 1 30.81 ? O3G GTP 604 F 1 
HETATM 5 O O3B GTP . . . IA 4 6.016 -16.326 49.588 1 27.84 ? O3B GTP 604 F 1 
HETATM 6 P PB GTP . . . IA 4 5.763 -14.914 48.876 1 25.03 ? PB GTP 604 F 1 
HETATM 7 O O1B GTP . . . IA 4 6.36 -14.856 47.473 1 22.49 ? O1B GTP 604 F 1 
HETATM 8 O O2B GTP . . . IA 4 4.336 -14.443 48.923 1 19.94 ? O2B GTP 604 F 1 
HETATM 9 O O3A GTP . . . IA 4 6.636 -13.982 49.845 1 34.39 ? O3A GTP 604 F 1 
HETATM 10 P PA GTP . . . IA 4 6.379 -13.86 51.423 1 28.97 ? PA GTP 604 F 1 
HETATM 11 O O1A GTP . . . IA 4 6.567 -12.385 51.715 1 27.42 ? O1A GTP 604 F 1 
HETATM 12 O O2A GTP . . . IA 4 5.012 -14.373 51.768 1 23.21 ? O2A GTP 604 F 1 
HETATM 13 O O5' GTP . . . IA 4 7.52 -14.72 52.15 1 18.24 ? O5' GTP 604 F 1 
HETATM 14 C C5' GTP . . . IA 4 8.82 -14.156 52.125 1 18.98 ? C5' GTP 604 F 1 
HETATM 15 C C4' GTP . . . IA 4 9.845 -15.15 51.6 1 19.26 ? C4' GTP 604 F 1 
HETATM 16 O O4' GTP . . . IA 4 10.077 -16.106 52.617 1 22.58 ? O4' GTP 604 F 1 
HETATM 17 C C3' GTP . . . IA 4 9.362 -15.928 50.399 1 21.68 ? C3' GTP 604 F 1 
HETATM 18 O O3' GTP . . . IA 4 10.492 -16.339 49.686 1 19.12 ? O3' GTP 604 F 1 
HETATM 19 C C2' GTP . . . IA 4 8.791 -17.191 50.983 1 24.45 ? C2' GTP 604 F 1 
HETATM 20 O O2' GTP . . . IA 4 9.018 -18.289 50.158 1 25.61 ? O2' GTP 604 F 1 
HETATM 21 C C1' GTP . . . IA 4 9.588 -17.389 52.25 1 23.63 ? C1' GTP 604 F 1 
HETATM 22 N N9 GTP . . . IA 4 8.688 -17.988 53.272 1 27.18 ? N9 GTP 604 F 1 
HETATM 23 C C8 GTP . . . IA 4 7.342 -17.762 53.51 1 22.34 ? C8 GTP 604 F 1 
HETATM 24 N N7 GTP . . . IA 4 6.941 -18.551 54.544 1 17.59 ? N7 GTP 604 F 1 
HETATM 25 C C5 GTP . . . IA 4 8.007 -19.27 54.957 1 19.54 ? C5 GTP 604 F 1 
HETATM 26 C C6 GTP . . . IA 4 8.182 -20.218 55.951 1 21.88 ? C6 GTP 604 F 1 
HETATM 27 O O6 GTP . . . IA 4 7.232 -20.544 56.663 1 20.97 ? O6 GTP 604 F 1 
HETATM 28 N N1 GTP . . . IA 4 9.437 -20.792 56.126 1 21.68 ? N1 GTP 604 F 1 
HETATM 29 C C2 GTP . . . IA 4 10.501 -20.426 55.321 1 19.31 ? C2 GTP 604 F 1 
HETATM 30 N N2 GTP . . . IA 4 11.697 -20.968 55.48 1 19.76 ? N2 GTP 604 F 1 
HETATM 31 N N3 GTP . . . IA 4 10.327 -19.496 54.329 1 21.88 ? N3 GTP 604 F 1 
HETATM 32 C C4 GTP . . . IA 4 9.104 -18.932 54.164 1 25.25 ? C4 GTP 604 F 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           32 
#